5FIW

CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE AT 1.7 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb5FIW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2015-10-02 Released: 2015-10-14
Deposition Author(s): Bonnefond, L., Cavarelli, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.193
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

Literature

Crystal Structure of Human Myeloperoxidase at 1.7 Angstroms Resolution

Bonnefond, L., Cavarelli, J.

To be published.

Macromolecule Content

Total Structure Weight: 134.94 kDa
Atom Count: 10,331
Modelled Residue Count: 1,136
Deposited Residue Count: 1,142
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYELOPEROXIDASE	A, B	105	Homo sapiens	Mutation(s): 0 EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens) Explore P05164 Go to UniProtKB: P05164
PHAROS: P05164 GTEx: ENSG00000005381
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05164
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MYELOPEROXIDASE	C, D	466	Homo sapiens	Mutation(s): 0 EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens) Explore P05164 Go to UniProtKB: P05164
PHAROS: P05164 GTEx: ENSG00000005381
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05164
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C Focus chain D	Go to GlyGen: P05164-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	5		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B]	H [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	N [auth C], O [auth C], R [auth D], S [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	P [auth C], T [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain P [auth C] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain U [auth D] MOL2 format, chain K [auth C] MOL2 format, chain U [auth D] mmCIF format, chain K [auth C] mmCIF format, chain U [auth D]	K [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain U [auth D] Interactions & Density Focus chain K [auth C] Focus chain U [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	G [auth A], I [auth B], L [auth C], M [auth C], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	C, D	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.193
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.16	α = 90
b = 105.16	β = 90
c = 225.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Bonnefond, L.

Cavarelli, J.

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary

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5FIW

CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE AT 1.7 ANGSTROMS RESOLUTION

Crystal Structure of Human Myeloperoxidase at 1.7 Angstroms Resolution

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2