1QIB | pdb_00001qib

CRYSTAL STRUCTURE OF GELATINASE A CATALYTIC DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1QIB/pdb

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


• Deposited: 1999-06-11 Released: 1999-11-19 
• Deposition Author(s): Dhanaraj, V., Williams, M.G., Ye, Q.-Z., Molina, F., Johnson, L.L., Ortwine, D.F., Pavlovsky, A., Rubin, J.R., Skeean, R.W., White, A.D., Humblet, C., Hupe, D.J., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.244 (Depositor) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

X-ray structure of gelatinase A catalytic domain complexed with a hydroxamate inhibitor

Dhanaraj, V., Williams, M.G., Ye, Q.-Z., Molina, F., Johnson, L.L., Ortwine, D.F., Pavlovsky, A., Rubin, J.R., Skeean, R.W., White, A.D., Humblet, C., Hupe, D.J., Blundell, T.L.

(1999) Croat Chem Acta 72: 575-591

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.21 kDa 
• Atom Count: 1,282 
• Modeled Residue Count: 161 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
72 kDa type IV collagenase	A	161	Homo sapiens	Mutation(s): 0  Gene Names: MMP2, CLG4A EC: 3.4.24.24
UniProt & NIH Common Fund Data Resources
Find proteins for P08253 (Homo sapiens) Explore P08253  Go to UniProtKB:  P08253
PHAROS:  P08253 GTEx:  ENSG00000087245

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.244 (Depositor) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.83	α = 90
b = 84.83	β = 90
c = 57.9	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-19 
Deposition Author(s): Dhanaraj, V., Williams, M.G., Ye, Q.-Z., Molina, F., Johnson, L.L., Ortwine, D.F., Pavlovsky, A., Rubin, J.R., Skeean, R.W., White, A.D., Humblet, C., Hupe, D.J., Blundell, T.L.

Revision History  

• Version 1.0: 1999-11-19
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-05-31
  Changes: Database references, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations