5B3S

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

PDB DOI: https://doi.org/10.2210/pdb5B3S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2016-03-11 Released: 2017-03-22
Deposition Author(s): Shimada, A., Shinzawa-Ito, K., Yoshikawa, S., Tsukihara, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.177
R-Value Work: 0.153
R-Value Observed: 0.154

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

Shimada, A., Muramoto, K., Shinzawa-Ito, K., Yoshikawa, S., Tsukihara, T.

To be published.

Macromolecule Content

Total Structure Weight: 451.59 kDa
Atom Count: 34,917
Modelled Residue Count: 3,550
Deposited Residue Count: 3,550
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00396
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68530
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	259	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00415
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D, Q	144	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00423
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	E, R	105	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00426
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F, S	94	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00428
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2, mitochondrial	G, T	84	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	79	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
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UniProt Group	P00429
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
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UniProt Group	P04038
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	J, W	58	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
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UniProt Group	P07470
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	K, X	49	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
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UniProt Group	P13183
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	46	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00430
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B, mitochondrial	M, Z	43	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10175
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Reference Sequence

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain LB [auth C] SDF format, chain LC [auth G] SDF format, chain XF [auth T] SDF format, chain YE [auth P] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth G] MOL2 format, chain XF [auth T] MOL2 format, chain YE [auth P] mmCIF format, chain LB [auth C] mmCIF format, chain LC [auth G] mmCIF format, chain XF [auth T] mmCIF format, chain YE [auth P]	LB [auth C], LC [auth G], XF [auth T], YE [auth P]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain LB [auth C] Focus chain LC [auth G] Focus chain XF [auth T] Focus chain YE [auth P] Interactions & Density Focus chain LB [auth C] Focus chain LC [auth G] Focus chain XF [auth T] Focus chain YE [auth P]
TGL Query on TGL Download Ideal Coordinates CCD File SDF format, chain DD [auth L] SDF format, chain JF [auth Q] SDF format, chain LG [auth Y] SDF format, chain TD [auth N] SDF format, chain WA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain DD [auth L] MOL2 format, chain JF [auth Q] MOL2 format, chain LG [auth Y] MOL2 format, chain TD [auth N] MOL2 format, chain WA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain DD [auth L] mmCIF format, chain JF [auth Q] mmCIF format, chain LG [auth Y] mmCIF format, chain TD [auth N] mmCIF format, chain WA [auth B] mmCIF format, chain ZA [auth B]	DD [auth L] JF [auth Q] LG [auth Y] TD [auth N] WA [auth B] DD [auth L], JF [auth Q], LG [auth Y], TD [auth N], WA [auth B], ZA [auth B]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain DD [auth L] Focus chain JF [auth Q] Focus chain LG [auth Y] Focus chain TD [auth N] Focus chain WA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain DD [auth L] Focus chain JF [auth Q] Focus chain LG [auth Y] Focus chain TD [auth N] Focus chain WA [auth B] Focus chain ZA [auth B]
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain MD [auth N] SDF format, chain ND [auth N] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain MD [auth N] MOL2 format, chain ND [auth N] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain MD [auth N] mmCIF format, chain ND [auth N]	AA [auth A], BA [auth A], MD [auth N], ND [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain MD [auth N] Focus chain ND [auth N] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain MD [auth N] Focus chain ND [auth N]
PEK Query on PEK Download Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain UE [auth P] SDF format, chain VE [auth P] SDF format, chain WE [auth P] SDF format, chain WF [auth T] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain UE [auth P] MOL2 format, chain VE [auth P] MOL2 format, chain WE [auth P] MOL2 format, chain WF [auth T] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain UE [auth P] mmCIF format, chain VE [auth P] mmCIF format, chain WE [auth P] mmCIF format, chain WF [auth T]	HB [auth C] IB [auth C] UE [auth P] VE [auth P] WE [auth P] HB [auth C], IB [auth C], UE [auth P], VE [auth P], WE [auth P], WF [auth T]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C₄₃ H₇₈ N O₈ P ANRKEHNWXKCXDB-BHFWLYLHSA-N		Interactions Focus chain HB [auth C] Focus chain IB [auth C] Focus chain UE [auth P] Focus chain VE [auth P] Focus chain WE [auth P] Focus chain WF [auth T] Interactions & Density Focus chain HB [auth C] Focus chain IB [auth C] Focus chain UE [auth P] Focus chain VE [auth P] Focus chain WE [auth P] Focus chain WF [auth T]
PSC Query on PSC Download Ideal Coordinates CCD File SDF format, chain NE [auth O] SDF format, chain YA [auth B] MOL2 format, chain NE [auth O] MOL2 format, chain YA [auth B] mmCIF format, chain NE [auth O] mmCIF format, chain YA [auth B]	NE [auth O], YA [auth B]	(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE C₄₂ H₈₁ N O₈ P JLPULHDHAOZNQI-AUSZDXHESA-O		Interactions Focus chain NE [auth O] Focus chain YA [auth B] Interactions & Density Focus chain NE [auth O] Focus chain YA [auth B]
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain OC [auth G] SDF format, chain SD [auth N] SDF format, chain UD [auth N] SDF format, chain XE [auth P] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain OC [auth G] MOL2 format, chain SD [auth N] MOL2 format, chain UD [auth N] MOL2 format, chain XE [auth P] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth C] mmCIF format, chain OC [auth G] mmCIF format, chain SD [auth N] mmCIF format, chain UD [auth N] mmCIF format, chain XE [auth P]	GA [auth A] HA [auth A] JB [auth C] KB [auth C] OC [auth G] GA [auth A], HA [auth A], JB [auth C], KB [auth C], OC [auth G], SD [auth N], UD [auth N], XE [auth P]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain OC [auth G] Focus chain SD [auth N] Focus chain UD [auth N] Focus chain XE [auth P] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain OC [auth G] Focus chain SD [auth N] Focus chain UD [auth N] Focus chain XE [auth P]
DMU Query on DMU Download Ideal Coordinates CCD File SDF format, chain AD [auth K] SDF format, chain BD [auth K] SDF format, chain BF [auth P] SDF format, chain CD [auth K] SDF format, chain ED [auth L] SDF format, chain FG [auth X] SDF format, chain GD [auth M] SDF format, chain GG [auth X] SDF format, chain HG [auth X] SDF format, chain IF [auth P] SDF format, chain IG [auth X] SDF format, chain JG [auth X] SDF format, chain LD [auth M] SDF format, chain MB [auth C] SDF format, chain MC [auth G] SDF format, chain NB [auth C] SDF format, chain NG [auth Z] SDF format, chain OE [auth O] SDF format, chain XC [auth K] SDF format, chain YC [auth K] SDF format, chain YF [auth T] SDF format, chain ZC [auth K] SDF format, chain ZE [auth P] MOL2 format, chain AD [auth K] MOL2 format, chain BD [auth K] MOL2 format, chain BF [auth P] MOL2 format, chain CD [auth K] MOL2 format, chain ED [auth L] MOL2 format, chain FG [auth X] MOL2 format, chain GD [auth M] MOL2 format, chain GG [auth X] MOL2 format, chain HG [auth X] MOL2 format, chain IF [auth P] MOL2 format, chain IG [auth X] MOL2 format, chain JG [auth X] MOL2 format, chain LD [auth M] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth G] MOL2 format, chain NB [auth C] MOL2 format, chain NG [auth Z] MOL2 format, chain OE [auth O] MOL2 format, chain XC [auth K] MOL2 format, chain YC [auth K] MOL2 format, chain YF [auth T] MOL2 format, chain ZC [auth K] MOL2 format, chain ZE [auth P] mmCIF format, chain AD [auth K] mmCIF format, chain BD [auth K] mmCIF format, chain BF [auth P] mmCIF format, chain CD [auth K] mmCIF format, chain ED [auth L] mmCIF format, chain FG [auth X] mmCIF format, chain GD [auth M] mmCIF format, chain GG [auth X] mmCIF format, chain HG [auth X] mmCIF format, chain IF [auth P] mmCIF format, chain IG [auth X] mmCIF format, chain JG [auth X] mmCIF format, chain LD [auth M] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth G] mmCIF format, chain NB [auth C] mmCIF format, chain NG [auth Z] mmCIF format, chain OE [auth O] mmCIF format, chain XC [auth K] mmCIF format, chain YC [auth K] mmCIF format, chain YF [auth T] mmCIF format, chain ZC [auth K] mmCIF format, chain ZE [auth P]	AD [auth K] BD [auth K] BF [auth P] CD [auth K] ED [auth L] AD [auth K], BD [auth K], BF [auth P], CD [auth K], ED [auth L], FG [auth X], GD [auth M], GG [auth X], HG [auth X], IF [auth P], IG [auth X], JG [auth X], LD [auth M], MB [auth C], MC [auth G], NB [auth C], NG [auth Z], OE [auth O], XC [auth K], YC [auth K], YF [auth T], ZC [auth K], ZE [auth P]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain AD [auth K] Focus chain BD [auth K] Focus chain BF [auth P] Focus chain CD [auth K] Focus chain ED [auth L] Focus chain FG [auth X] Focus chain GD [auth M] Focus chain GG [auth X] Focus chain HG [auth X] Focus chain IF [auth P] Focus chain IG [auth X] Focus chain JG [auth X] Focus chain LD [auth M] Focus chain MB [auth C] Focus chain MC [auth G] Focus chain NB [auth C] Focus chain NG [auth Z] Focus chain OE [auth O] Focus chain XC [auth K] Focus chain YC [auth K] Focus chain YF [auth T] Focus chain ZC [auth K] Focus chain ZE [auth P] Interactions & Density Focus chain AD [auth K] Focus chain BD [auth K] Focus chain BF [auth P] Focus chain CD [auth K] Focus chain ED [auth L] Focus chain FG [auth X] Focus chain GD [auth M] Focus chain GG [auth X] Focus chain HG [auth X] Focus chain IF [auth P] Focus chain IG [auth X] Focus chain JG [auth X] Focus chain LD [auth M] Focus chain MB [auth C] Focus chain MC [auth G] Focus chain NB [auth C] Focus chain NG [auth Z] Focus chain OE [auth O] Focus chain XC [auth K] Focus chain YC [auth K] Focus chain YF [auth T] Focus chain ZC [auth K] Focus chain ZE [auth P]
CHD Query on CHD Download Ideal Coordinates CCD File SDF format, chain AF [auth P] SDF format, chain EG [auth W] SDF format, chain GB [auth C] SDF format, chain KG [auth Y] SDF format, chain NC [auth G] SDF format, chain TC [auth J] SDF format, chain TE [auth P] SDF format, chain UC [auth J] SDF format, chain VF [auth T] MOL2 format, chain AF [auth P] MOL2 format, chain EG [auth W] MOL2 format, chain GB [auth C] MOL2 format, chain KG [auth Y] MOL2 format, chain NC [auth G] MOL2 format, chain TC [auth J] MOL2 format, chain TE [auth P] MOL2 format, chain UC [auth J] MOL2 format, chain VF [auth T] mmCIF format, chain AF [auth P] mmCIF format, chain EG [auth W] mmCIF format, chain GB [auth C] mmCIF format, chain KG [auth Y] mmCIF format, chain NC [auth G] mmCIF format, chain TC [auth J] mmCIF format, chain TE [auth P] mmCIF format, chain UC [auth J] mmCIF format, chain VF [auth T]	AF [auth P] EG [auth W] GB [auth C] KG [auth Y] NC [auth G] AF [auth P], EG [auth W], GB [auth C], KG [auth Y], NC [auth G], TC [auth J], TE [auth P], UC [auth J], VF [auth T]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain AF [auth P] Focus chain EG [auth W] Focus chain GB [auth C] Focus chain KG [auth Y] Focus chain NC [auth G] Focus chain TC [auth J] Focus chain TE [auth P] Focus chain UC [auth J] Focus chain VF [auth T] Interactions & Density Focus chain AF [auth P] Focus chain EG [auth W] Focus chain GB [auth C] Focus chain KG [auth Y] Focus chain NC [auth G] Focus chain TC [auth J] Focus chain TE [auth P] Focus chain UC [auth J] Focus chain VF [auth T]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain ME [auth O] SDF format, chain XA [auth B] MOL2 format, chain ME [auth O] MOL2 format, chain XA [auth B] mmCIF format, chain ME [auth O] mmCIF format, chain XA [auth B]	ME [auth O], XA [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain ME [auth O] Focus chain XA [auth B] Interactions & Density Focus chain ME [auth O] Focus chain XA [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CG [auth U] SDF format, chain RC [auth H] MOL2 format, chain CG [auth U] MOL2 format, chain RC [auth H] mmCIF format, chain CG [auth U] mmCIF format, chain RC [auth H]	CG [auth U], RC [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CG [auth U] Focus chain RC [auth H] Interactions & Density Focus chain CG [auth U] Focus chain RC [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain FC [auth F] SDF format, chain PF [auth S] MOL2 format, chain FC [auth F] MOL2 format, chain PF [auth S] mmCIF format, chain FC [auth F] mmCIF format, chain PF [auth S]	FC [auth F], PF [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain FC [auth F] Focus chain PF [auth S] Interactions & Density Focus chain FC [auth F] Focus chain PF [auth S]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain OD [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain OD [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain OD [auth N]	CA [auth A], OD [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain OD [auth N] Interactions & Density Focus chain CA [auth A] Focus chain OD [auth N]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain AC [auth D] SDF format, chain AE [auth N] SDF format, chain AG [auth T] SDF format, chain BB [auth B] SDF format, chain BC [auth D] SDF format, chain BE [auth N] SDF format, chain BG [auth U] SDF format, chain CB [auth B] SDF format, chain CC [auth E] SDF format, chain CE [auth N] SDF format, chain CF [auth P] SDF format, chain DB [auth B] SDF format, chain DC [auth E] SDF format, chain DE [auth N] SDF format, chain DF [auth P] SDF format, chain DG [auth V] SDF format, chain EB [auth B] SDF format, chain EC [auth E] SDF format, chain EE [auth N] SDF format, chain EF [auth P] SDF format, chain FB [auth B] SDF format, chain FD [auth L] SDF format, chain FE [auth N] SDF format, chain FF [auth P] SDF format, chain GC [auth F] SDF format, chain GE [auth N] SDF format, chain GF [auth P] SDF format, chain HC [auth F] SDF format, chain HD [auth M] SDF format, chain HE [auth N] SDF format, chain HF [auth P] SDF format, chain IA [auth A] SDF format, chain IC [auth F] SDF format, chain ID [auth M] SDF format, chain IE [auth N] SDF format, chain JA [auth A] SDF format, chain JC [auth F] SDF format, chain JD [auth M] SDF format, chain JE [auth N] SDF format, chain KA [auth A] SDF format, chain KC [auth F] SDF format, chain KD [auth M] SDF format, chain KE [auth N] SDF format, chain KF [auth Q] SDF format, chain LA [auth A] SDF format, chain LE [auth N] SDF format, chain LF [auth Q] SDF format, chain MA [auth A] SDF format, chain MF [auth Q] SDF format, chain MG [auth Y] SDF format, chain NA [auth A] SDF format, chain NF [auth R] SDF format, chain OA [auth A] SDF format, chain OB [auth C] SDF format, chain OF [auth R] SDF format, chain PA [auth A] SDF format, chain PB [auth C] SDF format, chain PC [auth G] SDF format, chain PE [auth O] SDF format, chain QA [auth A] SDF format, chain QB [auth C] SDF format, chain QC [auth G] SDF format, chain QE [auth O] SDF format, chain QF [auth S] SDF format, chain RA [auth A] SDF format, chain RB [auth C] SDF format, chain RE [auth O] SDF format, chain RF [auth S] SDF format, chain SA [auth A] SDF format, chain SB [auth C] SDF format, chain SC [auth I] SDF format, chain SE [auth O] SDF format, chain SF [auth S] SDF format, chain TA [auth A] SDF format, chain TB [auth C] SDF format, chain TF [auth S] SDF format, chain UA [auth A] SDF format, chain UB [auth C] SDF format, chain UF [auth S] SDF format, chain VA [auth A] SDF format, chain VB [auth C] SDF format, chain VC [auth J] SDF format, chain VD [auth N] SDF format, chain WB [auth C] SDF format, chain WC [auth J] SDF format, chain WD [auth N] SDF format, chain XB [auth D] SDF format, chain XD [auth N] SDF format, chain YB [auth D] SDF format, chain YD [auth N] SDF format, chain ZB [auth D] SDF format, chain ZD [auth N] SDF format, chain ZF [auth T] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth D] MOL2 format, chain AE [auth N] MOL2 format, chain AG [auth T] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth D] MOL2 format, chain BE [auth N] MOL2 format, chain BG [auth U] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth E] MOL2 format, chain CE [auth N] MOL2 format, chain CF [auth P] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth E] MOL2 format, chain DE [auth N] MOL2 format, chain DF [auth P] MOL2 format, chain DG [auth V] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth E] MOL2 format, chain EE [auth N] MOL2 format, chain EF [auth P] MOL2 format, chain FB [auth B] MOL2 format, chain FD [auth L] MOL2 format, chain FE [auth N] MOL2 format, chain FF [auth P] MOL2 format, chain GC [auth F] MOL2 format, chain GE [auth N] MOL2 format, chain GF [auth P] MOL2 format, chain HC [auth F] MOL2 format, chain HD [auth M] MOL2 format, chain HE [auth N] MOL2 format, chain HF [auth P] MOL2 format, chain IA [auth A] MOL2 format, chain IC [auth F] MOL2 format, chain ID [auth M] MOL2 format, chain IE [auth N] MOL2 format, chain JA [auth A] MOL2 format, chain JC [auth F] MOL2 format, chain JD [auth M] MOL2 format, chain JE [auth N] MOL2 format, chain KA [auth A] MOL2 format, chain KC [auth F] MOL2 format, chain KD [auth M] MOL2 format, chain KE [auth N] MOL2 format, chain KF [auth Q] MOL2 format, chain LA [auth A] MOL2 format, chain LE [auth N] MOL2 format, chain LF [auth Q] MOL2 format, chain MA [auth A] MOL2 format, chain MF [auth Q] MOL2 format, chain MG [auth Y] MOL2 format, chain NA [auth A] MOL2 format, chain NF [auth R] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain OF [auth R] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth G] MOL2 format, chain PE [auth O] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth G] MOL2 format, chain QE [auth O] MOL2 format, chain QF [auth S] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth C] MOL2 format, chain RE [auth O] MOL2 format, chain RF [auth S] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth C] MOL2 format, chain SC [auth I] MOL2 format, chain SE [auth O] MOL2 format, chain SF [auth S] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain TF [auth S] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth C] MOL2 format, chain UF [auth S] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth C] MOL2 format, chain VC [auth J] MOL2 format, chain VD [auth N] MOL2 format, chain WB [auth C] MOL2 format, chain WC [auth J] MOL2 format, chain WD [auth N] MOL2 format, chain XB [auth D] MOL2 format, chain XD [auth N] MOL2 format, chain YB [auth D] MOL2 format, chain YD [auth N] MOL2 format, chain ZB [auth D] MOL2 format, chain ZD [auth N] MOL2 format, chain ZF [auth T] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth D] mmCIF format, chain AE [auth N] mmCIF format, chain AG [auth T] mmCIF format, chain BB [auth B] mmCIF format, chain BC [auth D] mmCIF format, chain BE [auth N] mmCIF format, chain BG [auth U] mmCIF format, chain CB [auth B] mmCIF format, chain CC [auth E] mmCIF format, chain CE [auth N] mmCIF format, chain CF [auth P] mmCIF format, chain DB [auth B] mmCIF format, chain DC [auth E] mmCIF format, chain DE [auth N] mmCIF format, chain DF [auth P] mmCIF format, chain DG [auth V] mmCIF format, chain EB [auth B] mmCIF format, chain EC [auth E] mmCIF format, chain EE [auth N] mmCIF format, chain EF [auth P] mmCIF format, chain FB [auth B] mmCIF format, chain FD [auth L] mmCIF format, chain FE [auth N] mmCIF format, chain FF [auth P] mmCIF format, chain GC [auth F] mmCIF format, chain GE [auth N] mmCIF format, chain GF [auth P] mmCIF format, chain HC [auth F] mmCIF format, chain HD [auth M] mmCIF format, chain HE [auth N] mmCIF format, chain HF [auth P] mmCIF format, chain IA [auth A] mmCIF format, chain IC [auth F] mmCIF format, chain ID [auth M] mmCIF format, chain IE [auth N] mmCIF format, chain JA [auth A] mmCIF format, chain JC [auth F] mmCIF format, chain JD [auth M] mmCIF format, chain JE [auth N] mmCIF format, chain KA [auth A] mmCIF format, chain KC [auth F] mmCIF format, chain KD [auth M] mmCIF format, chain KE [auth N] mmCIF format, chain KF [auth Q] mmCIF format, chain LA [auth A] mmCIF format, chain LE [auth N] mmCIF format, chain LF [auth Q] mmCIF format, chain MA [auth A] mmCIF format, chain MF [auth Q] mmCIF format, chain MG [auth Y] mmCIF format, chain NA [auth A] mmCIF format, chain NF [auth R] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth C] mmCIF format, chain OF [auth R] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain PC [auth G] mmCIF format, chain PE [auth O] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain QC [auth G] mmCIF format, chain QE [auth O] mmCIF format, chain QF [auth S] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth C] mmCIF format, chain RE [auth O] mmCIF format, chain RF [auth S] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth C] mmCIF format, chain SC [auth I] mmCIF format, chain SE [auth O] mmCIF format, chain SF [auth S] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth C] mmCIF format, chain TF [auth S] mmCIF format, chain UA [auth A] mmCIF format, chain UB [auth C] mmCIF format, chain UF [auth S] mmCIF format, chain VA [auth A] mmCIF format, chain VB [auth C] mmCIF format, chain VC [auth J] mmCIF format, chain VD [auth N] mmCIF format, chain WB [auth C] mmCIF format, chain WC [auth J] mmCIF format, chain WD [auth N] mmCIF format, chain XB [auth D] mmCIF format, chain XD [auth N] mmCIF format, chain YB [auth D] mmCIF format, chain YD [auth N] mmCIF format, chain ZB [auth D] mmCIF format, chain ZD [auth N] mmCIF format, chain ZF [auth T]	AB [auth B] AC [auth D] AE [auth N] AG [auth T] BB [auth B] AB [auth B], AC [auth D], AE [auth N], AG [auth T], BB [auth B], BC [auth D], BE [auth N], BG [auth U], CB [auth B], CC [auth E], CE [auth N], CF [auth P], DB [auth B], DC [auth E], DE [auth N], DF [auth P], DG [auth V], EB [auth B], EC [auth E], EE [auth N], EF [auth P], FB [auth B], FD [auth L], FE [auth N], FF [auth P], GC [auth F], GE [auth N], GF [auth P], HC [auth F], HD [auth M], HE [auth N], HF [auth P], IA [auth A], IC [auth F], ID [auth M], IE [auth N], JA [auth A], JC [auth F], JD [auth M], JE [auth N], KA [auth A], KC [auth F], KD [auth M], KE [auth N], KF [auth Q], LA [auth A], LE [auth N], LF [auth Q], MA [auth A], MF [auth Q], MG [auth Y], NA [auth A], NF [auth R], OA [auth A], OB [auth C], OF [auth R], PA [auth A], PB [auth C], PC [auth G], PE [auth O], QA [auth A], QB [auth C], QC [auth G], QE [auth O], QF [auth S], RA [auth A], RB [auth C], RE [auth O], RF [auth S], SA [auth A], SB [auth C], SC [auth I], SE [auth O], SF [auth S], TA [auth A], TB [auth C], TF [auth S], UA [auth A], UB [auth C], UF [auth S], VA [auth A], VB [auth C], VC [auth J], VD [auth N], WB [auth C], WC [auth J], WD [auth N], XB [auth D], XD [auth N], YB [auth D], YD [auth N], ZB [auth D], ZD [auth N], ZF [auth T]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain AC [auth D] Focus chain AE [auth N] Focus chain AG [auth T] Focus chain BB [auth B] Focus chain BC [auth D] Focus chain BE [auth N] Focus chain BG [auth U] Focus chain CB [auth B] Focus chain CC [auth E] Focus chain CE [auth N] Focus chain CF [auth P] Focus chain DB [auth B] Focus chain DC [auth E] Focus chain DE [auth N] Focus chain DF [auth P] Focus chain DG [auth V] Focus chain EB [auth B] Focus chain EC [auth E] Focus chain EE [auth N] Focus chain EF [auth P] Focus chain FB [auth B] Focus chain FD [auth L] Focus chain FE [auth N] Focus chain FF [auth P] Focus chain GC [auth F] Focus chain GE [auth N] Focus chain GF [auth P] Focus chain HC [auth F] Focus chain HD [auth M] Focus chain HE [auth N] Focus chain HF [auth P] Focus chain IA [auth A] Focus chain IC [auth F] Focus chain ID [auth M] Focus chain IE [auth N] Focus chain JA [auth A] Focus chain JC [auth F] Focus chain JD [auth M] Focus chain JE [auth N] Focus chain KA [auth A] Focus chain KC [auth F] Focus chain KD [auth M] Focus chain KE [auth N] Focus chain KF [auth Q] Focus chain LA [auth A] Focus chain LE [auth N] Focus chain LF [auth Q] Focus chain MA [auth A] Focus chain MF [auth Q] Focus chain MG [auth Y] Focus chain NA [auth A] Focus chain NF [auth R] Focus chain OA [auth A] Focus chain OB [auth C] Focus chain OF [auth R] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain PC [auth G] Focus chain PE [auth O] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain QC [auth G] Focus chain QE [auth O] Focus chain QF [auth S] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain RE [auth O] Focus chain RF [auth S] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain SC [auth I] Focus chain SE [auth O] Focus chain SF [auth S] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain TF [auth S] Focus chain UA [auth A] Focus chain UB [auth C] Focus chain UF [auth S] Focus chain VA [auth A] Focus chain VB [auth C] Focus chain VC [auth J] Focus chain VD [auth N] Focus chain WB [auth C] Focus chain WC [auth J] Focus chain WD [auth N] Focus chain XB [auth D] Focus chain XD [auth N] Focus chain YB [auth D] Focus chain YD [auth N] Focus chain ZB [auth D] Focus chain ZD [auth N] Focus chain ZF [auth T] Interactions & Density Focus chain AB [auth B] Focus chain AC [auth D] Focus chain AE [auth N] Focus chain AG [auth T] Focus chain BB [auth B] Focus chain BC [auth D] Focus chain BE [auth N] Focus chain BG [auth U] Focus chain CB [auth B] Focus chain CC [auth E] Focus chain CE [auth N] Focus chain CF [auth P] Focus chain DB [auth B] Focus chain DC [auth E] Focus chain DE [auth N] Focus chain DF [auth P] Focus chain DG [auth V] Focus chain EB [auth B] Focus chain EC [auth E] Focus chain EE [auth N] Focus chain EF [auth P] Focus chain FB [auth B] Focus chain FD [auth L] Focus chain FE [auth N] Focus chain FF [auth P] Focus chain GC [auth F] Focus chain GE [auth N] Focus chain GF [auth P] Focus chain HC [auth F] Focus chain HD [auth M] Focus chain HE [auth N] Focus chain HF [auth P] Focus chain IA [auth A] Focus chain IC [auth F] Focus chain ID [auth M] Focus chain IE [auth N] Focus chain JA [auth A] Focus chain JC [auth F] Focus chain JD [auth M] Focus chain JE [auth N] Focus chain KA [auth A] Focus chain KC [auth F] Focus chain KD [auth M] Focus chain KE [auth N] Focus chain KF [auth Q] Focus chain LA [auth A] Focus chain LE [auth N] Focus chain LF [auth Q] Focus chain MA [auth A] Focus chain MF [auth Q] Focus chain MG [auth Y] Focus chain NA [auth A] Focus chain NF [auth R] Focus chain OA [auth A] Focus chain OB [auth C] Focus chain OF [auth R] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain PC [auth G] Focus chain PE [auth O] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain QC [auth G] Focus chain QE [auth O] Focus chain QF [auth S] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain RE [auth O] Focus chain RF [auth S] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain SC [auth I] Focus chain SE [auth O] Focus chain SF [auth S] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain TF [auth S] Focus chain UA [auth A] Focus chain UB [auth C] Focus chain UF [auth S] Focus chain VA [auth A] Focus chain VB [auth C] Focus chain VC [auth J] Focus chain VD [auth N] Focus chain WB [auth C] Focus chain WC [auth J] Focus chain WD [auth N] Focus chain XB [auth D] Focus chain XD [auth N] Focus chain YB [auth D] Focus chain YD [auth N] Focus chain ZB [auth D] Focus chain ZD [auth N] Focus chain ZF [auth T]
CMO Query on CMO Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain RD [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain RD [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain RD [auth N]	FA [auth A], RD [auth N]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain RD [auth N] Interactions & Density Focus chain FA [auth A] Focus chain RD [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain PD [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain PD [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain PD [auth N]	DA [auth A], PD [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain PD [auth N] Interactions & Density Focus chain DA [auth A] Focus chain PD [auth N]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain QD [auth N] MOL2 format, chain EA [auth A] MOL2 format, chain QD [auth N] mmCIF format, chain EA [auth A] mmCIF format, chain QD [auth N]	EA [auth A], QD [auth N]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain QD [auth N] Interactions & Density Focus chain EA [auth A] Focus chain QD [auth N]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A, N	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
TPO Query on TPO	G, T	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR
SAC Query on SAC	I, V	L-PEPTIDE LINKING	C₅ H₉ N O₄		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.177
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.491	α = 90
b = 203.303	β = 90
c = 177.484	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
REFMAC	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06092

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 2.0: 2022-03-02
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Validate Data

Deposit Data

Help and Resources

5B3S

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

Entity ID: 1

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Entity ID: 12

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)