1Q3A

Crystal structure of the catalytic domain of human matrix metalloproteinase 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the catalytic domain of human matrix metalloproteinase 10.

Bertini, I.Calderone, V.Fragai, M.Luchinat, C.Mangani, S.Terni, B.

(2004) J Mol Biol 336: 707-716

  • DOI: 10.1016/j.jmb.2003.12.033
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The catalytic domain of matrix metalloproteinase-10 (MMP-10) has been expressed in Escherichia coli and its crystal structure solved at 2.1 A resolution. The availability of this structure allowed us to critically examine the small differences existing between the catalytic domains of MMP-3 and MMP-10, which show the highest sequence identity among all MMPs ...

    The catalytic domain of matrix metalloproteinase-10 (MMP-10) has been expressed in Escherichia coli and its crystal structure solved at 2.1 A resolution. The availability of this structure allowed us to critically examine the small differences existing between the catalytic domains of MMP-3 and MMP-10, which show the highest sequence identity among all MMPs. Furthermore, the binding mode of N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH), which is one of the most known commercial inhibitors of MMPs, is described for the first time.


    Related Citations: 
    • Development of New Hydroxamate Matrix Metalloproteinase Inhibitors Derived from Functionalized 4-Aminoprolines
      Natchus, M.G., Bookland, R.G., De, B., Almstead, N.G., Pikul, S., Janusz, M.J., Heitmeyer, S.A., Hookfin, E.B., Hsieh, L.C., Dowty, M.E., Dietsch, C.R., Patel, V.S., Garver, S.M., Gu, F., Pokross, M.E., Mieling, G.E., Baker, T.R., Foltz, D.J., Peng, S.X., Bornes, D.M., Strojnowski, M.J., Taiwo, Y.O.
      (2000) J Med Chem 43: 4948
    • Design, Synthesis, and Biological Evaluation of Potent Thiazine- and Thiazepine-Based Matrix Metalloproteinase Inhibitors
      Almstead, N.G., Bradley, R.S., Pikul, S., De, B., Natchus, M.G., Taiwo, Y.O., Gu, F., Williams, L.E., Hynd, B.A., Janusz, M.J., Dunaway, C.M., Mieling, G.E.
      (1999) J Med Chem 42: 4547

    Organizational Affiliation

    CERM, University of Florence and FiorGen Foundation, Via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. bertini@cerm.unifi.it



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stromelysin-2A, B, C165Homo sapiensMutation(s): 1 
Gene Names: MMP10 OR STMY2MMP10STMY2
EC: 3.4.24.22
Find proteins for P09238 (Homo sapiens)
Explore P09238 
Go to UniProtKB:  P09238
NIH Common Fund Data Resources
PHAROS  P09238
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGH
Query on NGH

Download CCD File 
A, B, C
N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID
C13 H20 N2 O5 S
JIRXORZYIXSWOB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGHKi:  132   nM  BindingDB
NGHKi:  133   nM  BindingDB
NGHIC50:  6500   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.152α = 90
b = 61.141β = 108.68
c = 68.588γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description