Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57314.74 
• Atom Count: 3824 
• Residue Count: 495 
• 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): 1 


• 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: 2.1 Å
• R-Value Free: 0.298 
• R-Value Work: 0.276 

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


• 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: 

• 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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Stromelysin-2	A, B, C	165	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NGH	A, B, C	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID C13 H20 N2 O5 S JIRXORZYIXSWOB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NGH	IC50: 6500 nM (84) BINDINGDB
NGH	Ki: 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 = 117.152	α = 90.00
b = 61.141	β = 108.68
c = 68.588	γ = 90.00

Software Package:

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