1Q3A

Crystal structure of the catalytic domain of human matrix metalloproteinase 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 

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

  • 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 existi ...

    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: 
    • 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
    • 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


    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-2
A, B, C
165Homo sapiensMutation(s): 1 
Gene Names: MMP10 (STMY2)
EC: 3.4.24.22
Find proteins for P09238 (Homo sapiens)
Go to Gene View: MMP10
Go to UniProtKB:  P09238
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NGH
Query on NGH

Download SDF File 
Download CCD File 
A, B, C
N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID
C13 H20 N2 O5 S
JIRXORZYIXSWOB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGHIC50: 6500 nM (84) BINDINGDB
NGHKi: 132 - 133 nM (84) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.152α = 90.00
b = 61.141β = 108.68
c = 68.588γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CCP4data scaling
SCALAdata scaling
REFMACrefinement
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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