Macromolecule Content

Total Structure Weight: 36.16 kDa
Atom Count: 3089
Residue Count: 320
Unique protein chains: 2

2OY2

Human MMP-8 in complex with peptide IAG

DOI: 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

wwPDB Validation 3D Report Full Report

This is version 1.3 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: 10.1002/anie.200603100
Primary Citation of Related Structures:
2OY2, 2OXZ, 2OXW, 2OXU, 2OY4

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil collagenase	A, F	158	Homo sapiens	Mutation(s): 0 Gene Names: MMP8, CLG1 EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens) Explore P22894 Go to UniProtKB: P22894
NIH Common Fund Data Resources
PHAROS P22894 GTEx ENSG00000118113
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-ALA-GLY peptide	W, Y	3	N/A	Mutation(s): 0
Protein Feature View 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 [A] SDF format, chain H [A] SDF format, chain K [F] SDF format, chain L [F] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain K [F] MOL2 format, chain L [F]	A, F	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [A] SDF format, chain I [F] SDF format, chain J [F] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain I [F] MOL2 format, chain J [F]	A, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2007-02-21
Released Date: 2007-03-06

Deposition Author(s):

Revision History

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.