4EFS

Human MMP12 in complex with L-glutamate motif inhibitor

Structural Biology Knowledgebase: 4EFS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.154

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4EFS

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18864.98

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A 159 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: MMP-12 catalitic subunit (UNP RESIDUES 106-263)
Mutation: F171D
Gene Name(s): MMP12 Gene View HME

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
E37
Query on E37

A N~2~-[4-(4-phenylthiophen-2-yl)benzoyl]-L- alpha-glutamine
C22 H20 N2 O4 S
ADDJDJQFPKUMAF-SFHVURJKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

A S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGR
Query on PGR

A R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
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)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-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 %)
E37 Ki: 2.5 nM (99) BindingDB

Ki: 2.5 nM  BindingMOAD
Ki: 2.5 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.154
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.97 α = 90.00
b = 63.19 β = 90.00
c = 37.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-30
  • 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