3ZS0

Human Myeloperoxidase inactivated by TX2

PDB DOI: https://doi.org/10.2210/pdb3ZS0/pdb

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

Deposited: 2011-06-21 Released: 2011-08-31
Deposition Author(s): Tiden, A.K., Sjogren, T., Svensson, M., Bernlind, A., Senthilmohan, R., Auchere, F., Norman, H., Markgren, P.O., Gustavsson, S., Schmidt, S., Lundquist, S., Forbes, L.V., Magon, N.J., Jameson, G.N., Eriksson, H., Kettle, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.207
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 136.72 kDa
Atom Count: 10,054
Modelled Residue Count: 1,140
Deposited Residue Count: 1,150
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 LIGHT CHAIN	A, B	108	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 HEAVY CHAIN	C, D	467	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

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	6		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-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	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain T [auth D] MOL2 format, chain I [auth C] MOL2 format, chain T [auth D]	I [auth C], T [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth C] Focus chain T [auth D] Interactions & Density Focus chain I [auth C] Focus chain T [auth D]
ZS0 Query on ZS0 Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain S [auth D] MOL2 format, chain H [auth C] MOL2 format, chain S [auth D]	H [auth C], S [auth D]	3-(4-FLUOROBENZYL)-2-THIOXO-1,2,3,7-TETRAHYDRO-6H-PURIN-6-ONE C₁₂ H₉ F N₄ O S GMNQNGTVFNOHLD-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth C] Focus chain S [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D]	J [auth C], K [auth C], U [auth D], V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain U [auth D] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain G [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	G [auth B], N [auth C], O [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain G [auth B] Focus chain N [auth C] Focus chain O [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	P [auth C] Q [auth C] R [auth C] W [auth D] X [auth D] P [auth C], Q [auth C], R [auth C], W [auth D], X [auth D], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain Z [auth D] MOL2 format, chain L [auth C] MOL2 format, chain Z [auth D]	L [auth C], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain Z [auth D] Interactions & Density Focus chain L [auth C] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain M [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain M [auth C]	AA [auth D], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain M [auth C] Interactions & Density Focus chain AA [auth D] Focus chain M [auth C]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
ZS0	BindingDB: 3ZS0	IC50: 200 (nM) from 1 assay(s)
ZS0	PDBBind: 3ZS0	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.207
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.905	α = 90
b = 64.111	β = 97.12
c = 111.452	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2012-08-15
Changes: Database references
Version 1.2: 2012-08-29
Changes: Atomic model, Derived calculations, Other
Version 1.3: 2015-01-21
Changes: Atomic model, Derived calculations, Non-polymer description, Other
Version 1.4: 2018-01-17
Changes: Data collection
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: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3ZS0

Human Myeloperoxidase inactivated by TX2

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2