Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B).

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 

Starting Model: experimental
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Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase.

Elkins, P.A.Ho, Y.S.Smith, W.W.Janson, C.A.D'Alessio, K.J.McQueney, M.S.Cummings, M.D.Romanic, A.M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1182-1192

  • DOI: https://doi.org/10.1107/s0907444902007849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The X-ray crystal structure of the proform of human matrix metalloproteinase MMP9 has been solved to 2.5 A resolution. The construct includes the prodomain, the catalytic domain and three FnII (fibronectin type II) domains. The prodomain is inserted into the active-site cleft, blocking access to the catalytic zinc. Comparison with the crystal structure of the most closely related MMP, MMP2, indicates that the conformations of residues in the active-site cleft and in the cysteine-switch peptide of the prodomain are highly conserved and that design of MMP9-specific inhibitors will be challenging. In common with MMP2, the MMP9 S1' inhibitor-binding pocket is large compared with that of other MMPs. One small point of difference in the S1' binding pockets of MMP9 and MMP2 may provide an opportunity to explore the design of specific inhibitors. The side chain of Arg424 in MMP9 is angled slightly away from the S1' pocket when compared with the corresponding residue in MMP2, Thr424. The secondary structure of the FnII domains is conserved between the two closely related MMPs, although the second FnII domain makes no contact with the catalytic domain in MMP9, while the same domain in MMP2 has a substantial area of interaction with the catalytic domain.

  • Organizational Affiliation

    GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA. patricia_a_elkins@gsk.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9425Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.685α = 90
b = 123.685β = 90
c = 89.937γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description