Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 18082.96 
• Atom Count: 1267 
• Residue Count: 158 
• Unique protein chains: 1

3EHX

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid

• DOI: 10.2210/pdb3EHX/pdb

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


• Deposited: 2008-09-15 Released: 2009-05-19 
• Deposition Author(s): Calderone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.201 
• R-Value Work: 0.163 

Literature

Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties

Dragoni, E., Calderone, V., Fragai, M., Jaiswal, R., Luchinat, C., Nativi, C.

(2009) Bioconjug.Chem. 20: 719-727

• PubMed: 19275207 
• DOI: 10.1021/bc8003827
• Primary Citation of Related Structures:  
  3EHY


• PubMed Abstract: 
  

The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the designed BTI toward five different MMPs has been evaluated and the simultaneous formation of a highly stable ternary system Avidin-BTI-MMP clearly assessed. This system will permit the development of new approaches to detect, quantify, or collect MMPs in biological samples, with potential applications in vivo.

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Related Citations: 

• X-ray structures of binary and ternary enzyme-product-inhibitor complexes of matrix metalloproteinases
  Bertini, I.,Calderone, V.,Fragai, M.,Luchinat, C.,Mangani, S.,Terni, B.
  (2003) Angew.Chem.Int.Ed.Engl. 42: 2673




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Organizational Affiliation: 

Magnetic Resonance Center - University of Florence, Sesto Fiorentino, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Macrophage metalloelastase	A	158	Homo sapiens	Mutation(s): 1  Gene Names: MMP12 (HME) EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens) Go to Gene View: MMP12 Go to UniProtKB:  P39900

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
BDL	A	N-(biphenyl-4-ylsulfonyl)-D-leucine (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid C18 H21 N O4 S FBSVJQQVDISETN-QGZVFWFLSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BDL	Ki: 25 nM BINDINGMOAD
BDL	Ki: 25 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.201 
• R-Value Work: 0.163 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 51.181	α = 90.00
b = 60.554	β = 115.90
c = 54.428	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
MOSFLM	data reduction
CrysalisPro	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-15 
• Released Date: 2009-05-19 
• Deposition Author(s): Calderone, V.

Revision History 

• Version 1.0: 2009-05-19
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance