2OY2

Human MMP-8 in complex with peptide IAG

PDB DOI: https://doi.org/10.2210/pdb2OY2/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-02-21 Released: 2007-03-06
Deposition Author(s): Calderone, V., Bertini, I., Fragai, M., Luchinat, C., Maletta, M., Yeo, K.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.192
R-Value Work: 0.164
R-Value Observed: 0.166

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Snapshots of the reaction mechanism of matrix metalloproteinases.

Bertini, I., Calderone, V., Fragai, M., Luchinat, C., Maletta, M., Yeo, K.J.

(2006) Angew Chem Int Ed Engl 45: 7952-7955

PubMed: 17096442 Search on PubMed
DOI: https://doi.org/10.1002/anie.200603100
Primary Citation of Related Structures:
2OXU, 2OXW, 2OXZ, 2OY2, 2OY4

Organizational Affiliation

Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. [email protected]

Macromolecule Content

Total Structure Weight: 36.16 kDa
Atom Count: 3,089
Modelled Residue Count: 320
Deposited Residue Count: 322
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil collagenase	A, C [auth F]	158	Homo sapiens	Mutation(s): 0 Gene Names: MMP8, CLG1 EC: 3.4.24.34
UniProt & NIH Common Fund Data Resources
Find proteins for P22894 (Homo sapiens) Explore P22894 Go to UniProtKB: P22894
PHAROS: P22894 GTEx: ENSG00000118113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22894
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-ALA-GLY peptide	B [auth W], D [auth Y]	3	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth F] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth F] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth F] mmCIF format, chain L [auth F]	G [auth A], H [auth A], K [auth F], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth F] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth F] Focus chain L [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth F] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth F] MOL2 format, chain J [auth F] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth F] mmCIF format, chain J [auth F] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth F]	E [auth A], F [auth A], I [auth F], J [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth F] Focus chain J [auth F] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth F] Focus chain J [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.192
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.207	α = 90
b = 68.533	β = 98.1
c = 78.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-03-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-03-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

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Deposit Data

Help and Resources

2OY2

Human MMP-8 in complex with peptide IAG

Snapshots of the reaction mechanism of matrix metalloproteinases.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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