2D1N

Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453

Kohno, T.Hochigai, H.Yamashita, E.Tsukihara, T.Kanaoka, M.

(2006) Biochem Biophys Res Commun 344: 315-322

  • DOI: 10.1016/j.bbrc.2006.03.098
  • Primary Citation of Related Structures:  
    2D1O, 2D1N

  • PubMed Abstract: 
  • Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453 have been solved at 2.01 and 2.37A resolutions, respectively. The results revealed that the binding modes f ...

    Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453 have been solved at 2.01 and 2.37A resolutions, respectively. The results revealed that the binding modes for this inhibitor to MMP-3 and -13 were quite similar. However, subtle comparative differences were observed at the bottom of S1' pockets, which were occupied with the guanidinomethyl moiety of the inhibitor. A remarkable feature of the inhibitor was the deep penetration of its long aliphatic chain into the S1' pocket and exposure of the guanidinomethyl moiety to the solvent.


    Organizational Affiliation

    Drug Research Division, Dainippon Sumitomo Pharma Co., Ltd., 3-1-98 Kasugadenaka, Konohana-ku, Osaka 554-0022, Japan. tetsuya-kono@ds-pharma.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagenase 3AB166Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
NIH Common Fund Data Resources
PHAROS  P45452
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.47α = 90
b = 96.47β = 90
c = 67.52γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-07-18
    Changes: Data collection