Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.31 kDa 
• Atom Count: 4175 
• Residue Count: 471 
• Unique protein chains: 1

1Q3A

Crystal structure of the catalytic domain of human matrix metalloproteinase 10

• DOI: 10.2210/pdb1Q3A/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-07-29 Released: 2004-04-06 
• Deposition Author(s): Calderone, V., Bertini, I., Fragai, M., Luchinat, C., Mangani, S., Terni, B.

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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 

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

• PubMed: 15095982 
• 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. 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.

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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

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Organizational Affiliation: 

CERM, University of Florence and FiorGen Foundation, Via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Stromelysin-2	A, B, C	165	Homo sapiens	Mutation(s): 1  Gene Names: MMP10 OR STMY2, MMP10, STMY2 EC: 3.4.24.22
Find proteins for P09238 (Homo sapiens) Explore P09238  Go to UniProtKB:  P09238
NIH Common Fund Data Resources
PHAROS  P09238 GTEx  ENSG00000166670

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGH	A, B, C	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID C13 H20 N2 O5 S JIRXORZYIXSWOB-UHFFFAOYSA-N
ZN	A, B, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NGH	Ki:  132   nM  BindingDB
NGH	Ki:  133   nM  BindingDB
NGH	IC50:  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 = 117.152	α = 90
b = 61.141	β = 108.68
c = 68.588	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-29 
• Released Date: 2004-04-06 
Deposition Author(s): Calderone, V., Bertini, I., Fragai, M., Luchinat, C., Mangani, S., Terni, B.

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