Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39701.38 
• Atom Count: 2601 
• Residue Count: 349 
• Unique protein chains: 2

3V96

Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-1 (TIMP-1)

• DOI: 10.2210/pdb3V96/pdb

• Classification: HYDROLASE INHIBITOR/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): 1 


• Deposited: 2011-12-23 Released: 2012-03-28 
• Deposition Author(s): Batra, J., Soares, A.S., Radisky, E.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.266 
• R-Value Work: 0.215 

Literature

Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure.

Batra, J., Robinson, J., Soares, A.S., Fields, A.P., Radisky, D.C., Radisky, E.S.

(2012) J.Biol.Chem. 287: 15935-15946

• PubMed: 22427646 
• DOI: 10.1074/jbc.M112.341156


• PubMed Abstract: 
  

Matrix metalloproteinase 10 (MMP-10, stromelysin-2) is a secreted metalloproteinase with functions in skeletal development, wound healing, and vascular remodeling; its overexpression is also implicated in lung tumorigenesis and tumor progression. To understand the regulation of MMP-10 by tissue inhibitors of metalloproteinases (TIMPs), we have assessed equilibrium inhibition constants (K(i)) of putative physiological inhibitors TIMP-1 and TIMP-2 for the active catalytic domain of human MMP-10 (MMP-10cd) using multiple kinetic approaches. We find that TIMP-1 inhibits the MMP-10cd with a K(i) of 1.1 × 10(-9) M; this interaction is 10-fold weaker than the inhibition of the similar MMP-3 (stromelysin-1) catalytic domain (MMP-3cd) by TIMP-1. TIMP-2 inhibits the MMP-10cd with a K(i) of 5.8 × 10(-9) M, which is again 10-fold weaker than the inhibition of MMP-3cd by this inhibitor (K(i) = 5.5 × 10(-10) M). We solved the x-ray crystal structure of TIMP-1 bound to the MMP-10cd at 1.9 Å resolution; the structure was solved by molecular replacement and refined with an R-factor of 0.215 (R(free) = 0.266). Comparing our structure of MMP-10cd·TIMP-1 with the previously solved structure of MMP-3cd·TIMP-1 (Protein Data Bank entry 1UEA), we see substantial differences at the binding interface that provide insight into the differential binding of stromelysin family members to TIMP-1. This structural information may ultimately assist in the design of more selective TIMP-based inhibitors tailored for specificity toward individual members of the stromelysin family, with potential therapeutic applications.

---

Organizational Affiliation: 

Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Metalloproteinase inhibitor 1	A	184	Homo sapiens	Mutation(s): 1  Gene Names: TIMP1 (CLGI, TIMP)
Find proteins for P01033 (Homo sapiens) Go to Gene View: TIMP1 Go to UniProtKB:  P01033

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Stromelysin-2	B	165	Homo sapiens	Mutation(s): 0  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
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.266 
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 231.720	α = 90.00
b = 37.682	β = 90.00
c = 39.523	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
HKL-2000	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-23 
• Released Date: 2012-03-28 
• Deposition Author(s): Batra, J., Soares, A.S., Radisky, E.S.

Revision History 

• Version 1.0: 2012-03-28
  Type: Initial release
• Version 1.1: 2012-07-25
  Type: Database references