3TSK

Human MMP12 in complex with L-glutamate motif inhibitor

Structural Biology Knowledgebase: 3TSK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3TSK

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18431.47

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A 159 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: Catalitic subunit (UNP residues 106-263)
Mutation: F171D
Gene Name(s): MMP12 Gene View HME

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

A N~2~-{3-[4-(4-phenylthiophen-2-yl)phenyl]propanoyl}- L-glutaminyl-L-alpha-glutamine
C29 H32 N4 O6 S
KGPPRBTYRFIDAL-GOTSBHOMSA-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 %)
QEG Ki: 317 nM (99) BindingDB

N/A in BindingMoad
Kd: 67 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001060 (GLN,03J,GLU,NH2) A N~2~-{3-[4-(4-PHENYLTHIOPHEN-2-YL)PHENYL]PROPANOYL}-L-GLUTAMINYL-L-ALPHA-GLUTAMINE Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.162
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.71 α = 90.00
b = 63.06 β = 90.00
c = 37.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-13
  • Released Date: 2012-06-20
  • Deposition author(s): Stura, E.A., Dive, V., Devel, L., Czarny, B., Beau, F., Vera, L.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2012-10-17
    Type: Citation | Details: Citation update