1JJ9

Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate Recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 1JJ9

Classification: HYDROLASE

Total Structure Weight: 18654.08

Macromolecule Entities
Molecule Chains Length Organism Details
Matrix Metalloproteinase 8 A 163 Homo sapiens EC#: 3.4.24.34 IUBMB
Fragment: catalytic domain
Gene Name(s): MMP8 Gene View CLG1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-HYDROXY-5-[4-(2-HYDROXY-ETHYL)-PIPERIDIN- 1-YL]-5-PHENYL-1H-PYRIMIDINE-4,6-DIONE
C17 H21 N3 O4
IPBPOBHSNJFRFT-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 %)
BBT IC50: 1700 nM (100) BindingDB

IC50: 1700 nM  BindingMOAD
IC50: 1700 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.211
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 61.02 α = 90.00
b = 69.23 β = 90.00
c = 88.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-07-04
  • Released Date: 2001-08-01
  • Deposition author(s): Brandstetter, H., Grams, F., Glitz, D., Lang, A., Huber, R., Bode, W., Krell, H.-W., Engh, R.A.

Revision History

  • 2008-04-27
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance