3TVC

Human MMP13 in complex with L-glutamate motif inhibitor

Structural Biology Knowledgebase: 3TVC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 3TVC

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 20024.18

Macromolecule Entities
Molecule Chains Length Organism Details
Collagenase 3 A 169 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: MMP-13 catalytic subunit (UNP residues 104-272)
Gene Name(s): MMP13 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
E3P
Query on E3P

A N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]- L-alpha-glutamine
C26 H26 N2 O4
KNOYHJOPRUTPSQ-QHCPKHFHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
E3P Ki: 18 nM (100) BindingDB

Ki: 18 nM  BindingMOAD
Ki: 18 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.162
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.30 α = 90.00
b = 85.16 β = 90.00
c = 40.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-20
  • Released Date: 2012-06-20
  • Deposition author(s): Stura, E.A., Dive, V., Devel, L., Czarny, B., Beau, F., Vera, L., Cassar-Lajeunesse, E.

Revision History

  • 2012-10-17
    Type: Citation | Details: Citation update