1CK7

GELATINASE A (FULL-LENGTH)

• PDB DOI: https://doi.org/10.2210/pdb1CK7/pdb
• BMRB: 5262

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 1999-04-28 Released: 1999-08-25 
• Deposition Author(s): Morgunova, E., Tuuttila, A., Bergmann, U., Isupov, M., Lindqvist, Y., Schneider, G., Tryggvason, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.327 
• R-Value Work: 0.286 

Starting Models: experimental

Literature

Structure of human pro-matrix metalloproteinase-2: activation mechanism revealed.

Morgunova, E., Tuuttila, A., Bergmann, U., Isupov, M., Lindqvist, Y., Schneider, G., Tryggvason, K.

(1999) Science 284: 1667-1670

• PubMed: 10356396 
• DOI: https://doi.org/10.1126/science.284.5420.1667
• Primary Citation of Related Structures:  
  1CK7


• PubMed Abstract: 
  

  Matrix metalloproteinases (MMPs) catalyze extracellular matrix degradation. Control of their activity is a promising target for therapy of diseases characterized by abnormal connective tissue turnover. MMPs are expressed as latent proenzymes that are activated by proteolytic cleavage that triggers a conformational change in the propeptide (cysteine switch). The structure of proMMP-2 reveals how the propeptide shields the catalytic cleft and that the cysteine switch may operate through cleavage of loops essential for propeptide stability.

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Organizational Affiliation: 

Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.5 kDa 
• Atom Count: 5,051 
• Modelled Residue Count: 619 
• Deposited Residue Count: 631 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GELATINASE A)	A	631	Homo sapiens	Mutation(s): 1  EC: 3.4.24.24 Membrane Entity: Yes
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
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
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.327 
• R-Value Work: 0.286 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.32	α = 90
b = 121.32	β = 90
c = 345.11	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-25 
Deposition Author(s): Morgunova, E., Tuuttila, A., Bergmann, U., Isupov, M., Lindqvist, Y., Schneider, G., Tryggvason, K.

Revision History  

• Version 1.0: 1999-08-25
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2018-04-11
  Changes: Data collection
• Version 1.5: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.6: 2023-08-09
  Changes: Data collection, Refinement description
• Version 1.7: 2024-11-13
  Changes: Structure summary