8BEO

Crystal structure of E. coli glyoxylate carboligase mutant I393A with MAP

PDB DOI: https://doi.org/10.2210/pdb8BEO/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-10-21 Released: 2023-11-08
Deposition Author(s): Shaanan, B., Binshtein, E.
Funding Organization(s): United States - Israel Binational Science Foundation (BSF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.204
R-Value Work: 0.176
R-Value Observed: 0.177

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of E. coli glyoxylate carboligase mutant I393A with MAP

Shaanan, B., Binshtein, E.

To be published.

Macromolecule Content

Total Structure Weight: 417.09 kDa
Atom Count: 30,255
Modelled Residue Count: 3,552
Deposited Residue Count: 3,696
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate carboligase	A, B, C, D, E A, B, C, D, E, F	616	Escherichia coli K-12	Mutation(s): 1 Gene Names: gcl, b0507, JW0495 EC: 4.1.1.47
UniProt
Find proteins for P0AEP7 (Escherichia coli (strain K12)) Explore P0AEP7 Go to UniProtKB: P0AEP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain GA [auth B] SDF format, chain I [auth A] SDF format, chain OB [auth D] SDF format, chain ZB [auth E] SDF format, chain QC [auth F] MOL2 format, chain BB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain ZB [auth E] MOL2 format, chain QC [auth F] mmCIF format, chain BB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain ZB [auth E] mmCIF format, chain QC [auth F]	BB [auth C] GA [auth B] I [auth A] OB [auth D] QC [auth F] BB [auth C], GA [auth B], I [auth A], OB [auth D], QC [auth F], ZB [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BB [auth C] Focus chain GA [auth B] Focus chain I [auth A] Focus chain OB [auth D] Focus chain QC [auth F] Focus chain ZB [auth E] Interactions & Density Focus chain BB [auth C] Focus chain GA [auth B] Focus chain I [auth A] Focus chain OB [auth D] Focus chain QC [auth F] Focus chain ZB [auth E]
TDK (Subject of Investigation/LOI) Query on TDK Download Ideal Coordinates CCD File SDF format, chain AC [auth E] SDF format, chain CB [auth C] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain PB [auth D] SDF format, chain RC [auth F] MOL2 format, chain AC [auth E] MOL2 format, chain CB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain RC [auth F] mmCIF format, chain AC [auth E] mmCIF format, chain CB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain RC [auth F]	AC [auth E] CB [auth C] HA [auth B] J [auth A] PB [auth D] AC [auth E], CB [auth C], HA [auth B], J [auth A], PB [auth D], RC [auth F]	3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM C₁₅ H₂₆ N₄ O₁₁ P₃ S ILGXNMPRCMTAOK-HNNXBMFYSA-O		Interactions Focus chain AC [auth E] Focus chain CB [auth C] Focus chain HA [auth B] Focus chain J [auth A] Focus chain PB [auth D] Focus chain RC [auth F] Interactions & Density Focus chain AC [auth E] Focus chain CB [auth C] Focus chain HA [auth B] Focus chain J [auth A] Focus chain PB [auth D] Focus chain RC [auth F]
UQ0 Query on UQ0 Download Ideal Coordinates CCD File SDF format, chain BC [auth E] SDF format, chain DB [auth C] SDF format, chain JA [auth B] SDF format, chain L [auth A] SDF format, chain QB [auth D] SDF format, chain SC [auth F] MOL2 format, chain BC [auth E] MOL2 format, chain DB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain SC [auth F] mmCIF format, chain BC [auth E] mmCIF format, chain DB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain SC [auth F]	BC [auth E] DB [auth C] JA [auth B] L [auth A] QB [auth D] BC [auth E], DB [auth C], JA [auth B], L [auth A], QB [auth D], SC [auth F]	2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE C₉ H₁₀ O₄ UIXPTCZPFCVOQF-UHFFFAOYSA-N		Interactions Focus chain BC [auth E] Focus chain DB [auth C] Focus chain JA [auth B] Focus chain L [auth A] Focus chain QB [auth D] Focus chain SC [auth F] Interactions & Density Focus chain BC [auth E] Focus chain DB [auth C] Focus chain JA [auth B] Focus chain L [auth A] Focus chain QB [auth D] Focus chain SC [auth F]
DTU Query on DTU Download Ideal Coordinates CCD File SDF format, chain CC [auth E] MOL2 format, chain CC [auth E] mmCIF format, chain CC [auth E]	CC [auth E]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain CC [auth E] Interactions & Density Focus chain CC [auth E]
DTT Query on DTT Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	KA [auth B], O [auth A], P [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
ALU Query on ALU Download Ideal Coordinates CCD File SDF format, chain FB [auth C] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain RB [auth D] MOL2 format, chain FB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain RB [auth D] mmCIF format, chain FB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain RB [auth D]	FB [auth C], IA [auth B], K [auth A], RB [auth D]	METHYL HYDROGEN (S)-ACETYLPHOSPHONATE C₃ H₇ O₄ P QECABVMKPMRCRZ-UHFFFAOYSA-N		Interactions Focus chain FB [auth C] Focus chain IA [auth B] Focus chain K [auth A] Focus chain RB [auth D] Interactions & Density Focus chain FB [auth C] Focus chain IA [auth B] Focus chain K [auth A] Focus chain RB [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain GB [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain T [auth A] SDF format, chain TC [auth F] SDF format, chain V [auth A] SDF format, chain AA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TC [auth F] MOL2 format, chain V [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TC [auth F] mmCIF format, chain V [auth A] mmCIF format, chain AA [auth A]	AA [auth A] GB [auth C] M [auth A] N [auth A] NA [auth B] AA [auth A], GB [auth C], M [auth A], N [auth A], NA [auth B], T [auth A], TC [auth F], V [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain GB [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain T [auth A] Focus chain TC [auth F] Focus chain V [auth A] Interactions & Density Focus chain AA [auth A] Focus chain GB [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain T [auth A] Focus chain TC [auth F] Focus chain V [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AD [auth F] SDF format, chain CA [auth A] SDF format, chain DC [auth E] SDF format, chain EC [auth E] SDF format, chain FC [auth E] SDF format, chain GC [auth E] SDF format, chain HB [auth C] SDF format, chain JC [auth E] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain SB [auth D] SDF format, chain TB [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth D] SDF format, chain UC [auth F] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WC [auth F] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XC [auth F] SDF format, chain Y [auth A] SDF format, chain YC [auth F] SDF format, chain Z [auth A] SDF format, chain IB [auth C] SDF format, chain VC [auth F] MOL2 format, chain AD [auth F] MOL2 format, chain CA [auth A] MOL2 format, chain DC [auth E] MOL2 format, chain EC [auth E] MOL2 format, chain FC [auth E] MOL2 format, chain GC [auth E] MOL2 format, chain HB [auth C] MOL2 format, chain JC [auth E] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth D] MOL2 format, chain UC [auth F] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WC [auth F] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XC [auth F] MOL2 format, chain Y [auth A] MOL2 format, chain YC [auth F] MOL2 format, chain Z [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain VC [auth F] mmCIF format, chain AD [auth F] mmCIF format, chain CA [auth A] mmCIF format, chain DC [auth E] mmCIF format, chain EC [auth E] mmCIF format, chain FC [auth E] mmCIF format, chain GC [auth E] mmCIF format, chain HB [auth C] mmCIF format, chain JC [auth E] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SB [auth D] mmCIF format, chain TB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth D] mmCIF format, chain UC [auth F] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WC [auth F] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain XC [auth F] mmCIF format, chain Y [auth A] mmCIF format, chain YC [auth F] mmCIF format, chain Z [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain VC [auth F]	AD [auth F] CA [auth A] DC [auth E] EC [auth E] FC [auth E] AD [auth F], CA [auth A], DC [auth E], EC [auth E], FC [auth E], GC [auth E], HB [auth C], IB [auth C], JC [auth E], KB [auth C], LA [auth B], LB [auth C], MA [auth B], OA [auth B], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], SB [auth D], TB [auth D], U [auth A], UA [auth B], UB [auth D], UC [auth F], VA [auth B], VC [auth F], W [auth A], WC [auth F], X [auth A], XA [auth B], XC [auth F], Y [auth A], YC [auth F], Z [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AD [auth F] Focus chain CA [auth A] Focus chain DC [auth E] Focus chain EC [auth E] Focus chain FC [auth E] Focus chain GC [auth E] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JC [auth E] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain UC [auth F] Focus chain VA [auth B] Focus chain VC [auth F] Focus chain W [auth A] Focus chain WC [auth F] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XC [auth F] Focus chain Y [auth A] Focus chain YC [auth F] Focus chain Z [auth A] Interactions & Density Focus chain AD [auth F] Focus chain CA [auth A] Focus chain DC [auth E] Focus chain EC [auth E] Focus chain FC [auth E] Focus chain GC [auth E] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JC [auth E] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain UC [auth F] Focus chain VA [auth B] Focus chain VC [auth F] Focus chain W [auth A] Focus chain WC [auth F] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XC [auth F] Focus chain Y [auth A] Focus chain YC [auth F] Focus chain Z [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HC [auth E] MOL2 format, chain HC [auth E] mmCIF format, chain HC [auth E]	HC [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HC [auth E] Interactions & Density Focus chain HC [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain DA [auth A] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain NB [auth D] SDF format, chain NC [auth E] SDF format, chain OC [auth F] SDF format, chain PC [auth F] SDF format, chain ZA [auth B] SDF format, chain YB [auth E] MOL2 format, chain AB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain NC [auth E] MOL2 format, chain OC [auth F] MOL2 format, chain PC [auth F] MOL2 format, chain ZA [auth B] MOL2 format, chain YB [auth E] mmCIF format, chain AB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain NC [auth E] mmCIF format, chain OC [auth F] mmCIF format, chain PC [auth F] mmCIF format, chain ZA [auth B] mmCIF format, chain YB [auth E]	AB [auth C] DA [auth A] EA [auth B] EB [auth C] FA [auth B] AB [auth C], DA [auth A], EA [auth B], EB [auth C], FA [auth B], G [auth A], H [auth A], NB [auth D], NC [auth E], OC [auth F], PC [auth F], YB [auth E], ZA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain DA [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain NB [auth D] Focus chain NC [auth E] Focus chain OC [auth F] Focus chain PC [auth F] Focus chain YB [auth E] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain DA [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain NB [auth D] Focus chain NC [auth E] Focus chain OC [auth F] Focus chain PC [auth F] Focus chain YB [auth E] Focus chain ZA [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain IC [auth E] SDF format, chain JB [auth C] SDF format, chain KC [auth E] SDF format, chain LC [auth E] SDF format, chain MB [auth C] SDF format, chain MC [auth E] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain VB [auth D] SDF format, chain WA [auth B] SDF format, chain WB [auth D] SDF format, chain XB [auth D] SDF format, chain YA [auth B] SDF format, chain ZC [auth F] MOL2 format, chain BA [auth A] MOL2 format, chain IC [auth E] MOL2 format, chain JB [auth C] MOL2 format, chain KC [auth E] MOL2 format, chain LC [auth E] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth E] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain VB [auth D] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth D] MOL2 format, chain XB [auth D] MOL2 format, chain YA [auth B] MOL2 format, chain ZC [auth F] mmCIF format, chain BA [auth A] mmCIF format, chain IC [auth E] mmCIF format, chain JB [auth C] mmCIF format, chain KC [auth E] mmCIF format, chain LC [auth E] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth E] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain VB [auth D] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth D] mmCIF format, chain XB [auth D] mmCIF format, chain YA [auth B] mmCIF format, chain ZC [auth F]	BA [auth A] IC [auth E] JB [auth C] KC [auth E] LC [auth E] BA [auth A], IC [auth E], JB [auth C], KC [auth E], LC [auth E], MB [auth C], MC [auth E], SA [auth B], TA [auth B], VB [auth D], WA [auth B], WB [auth D], XB [auth D], YA [auth B], ZC [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain IC [auth E] Focus chain JB [auth C] Focus chain KC [auth E] Focus chain LC [auth E] Focus chain MB [auth C] Focus chain MC [auth E] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain VB [auth D] Focus chain WA [auth B] Focus chain WB [auth D] Focus chain XB [auth D] Focus chain YA [auth B] Focus chain ZC [auth F] Interactions & Density Focus chain BA [auth A] Focus chain IC [auth E] Focus chain JB [auth C] Focus chain KC [auth E] Focus chain LC [auth E] Focus chain MB [auth C] Focus chain MC [auth E] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain VB [auth D] Focus chain WA [auth B] Focus chain WB [auth D] Focus chain XB [auth D] Focus chain YA [auth B] Focus chain ZC [auth F]