3LJG

Human MMP12 in complex with non-zinc chelating inhibitor

Structural Biology Knowledgebase: 3LJG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3LJG

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 18990.05

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

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EEF
Query on EEF

A N-(3-biphenyl-4-ylpropanoyl)-L-alpha-glutamyl- L-alpha-glutamyl-amide
C25 H29 N3 O7
KGICPKKIUBLFER-PMACEKPBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P6G
Query on P6G

A HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HAE
Query on HAE

A ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-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 %)
EEF N/A in BindingDB
Ki: 18.6 nM  BindingMOAD
Ki: 18.6 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000805 (GLU,0YF,NH2) A N-(3-BIPHENYL-4-YLPROPANOYL)-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMYL-AMIDE Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.173
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.09 α = 90.00
b = 62.82 β = 90.00
c = 37.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-01-26
  • Released Date: 2010-09-01
  • Deposition author(s): Stura, E.A., Dive, V., Devel, L., Vera, L., Beau, F.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4