2OY2 | pdb_00002oy2

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1002/anie.200603100
• Primary Citation Related Structures: 
  2OXU, 2OXW, 2OXZ, 2OY2, 2OY4

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Organizational Affiliation: 
• Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth A], K [auth F], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], I [auth F], J [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

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

Entry History 

Deposition Data

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

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
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description