2OXZ | pdb_00002oxz

Human MMP-12 in complex with two peptides PQG and IAG

• PDB DOI: https://doi.org/10.2210/pdb2OXZ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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: 1.90 Å
• R-Value Free: 
  0.288 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.214 (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)

Macromolecule Content 

• Total Structure Weight: 18.43 kDa 
• Atom Count: 1,381 
• Modeled Residue Count: 163 
• Deposited Residue Count: 165 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	159	Homo sapiens	Mutation(s): 1  Gene Names: MMP12, HME EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
PHAROS:  P39900 GTEx:  ENSG00000262406

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PRO-GLN-GLY peptide	B [auth Y]	3	N/A	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-ALA-GLY peptide	C [auth X]	3	N/A	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.288 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.546	α = 90
b = 60.378	β = 115.41
c = 54.449	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	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: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description