3TT4

Human MMP8 in complex with L-glutamate motif inhibitor

Structural Biology Knowledgebase: 3TT4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3TT4

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18449.91

Macromolecule Entities
Molecule Chains Length Organism Details
Neutrophil collagenase A 159 Homo sapiens EC#: 3.4.24.34 IUBMB
Fragment: MMP8 catalytic domain (UNP residues 104-262)
Gene Name(s): MMP8 Gene View CLG1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
E1S
Query on E1S

A N~2~-{3-[4-(5-methylthiophen-2-yl)phenyl]propanoyl}- L-alpha-glutamine
C19 H22 N2 O4 S
XNDAUZRSIAEAAR-HNNXBMFYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
E1S Ki: 5.3 nM (100) BindingDB

Ki: 5.3 nM  BindingMOAD
Ki: 5.3 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.191
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 32.72 α = 90.00
b = 69.37 β = 90.00
c = 70.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-14
  • Released Date: 2012-06-20
  • Deposition author(s): Stura, E.A., Dive, V., Devel, L., Czarny, B., Beau, F., Vera, L.

Revision History

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