4JA1

Structure of MMP3 complexed with a platinum-based inhibitor

Structural Biology Knowledgebase: 4JA1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JA1

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 40378.87

Macromolecule Entities
Molecule Chains Length Organism Details
Stromelysin-1 A, B 173 Homo sapiens EC#: 3.4.24.17 IUBMB
Fragment: catalytic domain
Gene Name(s): MMP3 Gene View STMY1

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

B N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID
C13 H20 N2 O5 S
JIRXORZYIXSWOB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PT
Query on PT

A, B PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NGH IC50: 6500 nM (100) BindingDB
Ki: 132 - 133 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.195
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 38.12 α = 90.00
b = 77.61 β = 90.00
c = 106.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-18
  • Released Date: 2013-02-27
  • Deposition author(s): Belviso, B.D., Arnesano, F., Calderone, V., Caliandro, R., Natile, G., Siliqi, D.

Revision History

  • 2013-06-05
    Type: Citation | Details: Citation update
  • 2013-05-29
    Type: Function and keywords | Details: Update header and keywords
  • 2013-05-22
    Type: Citation | Details: Citation update
  • 2013-05-15
    Type: Citation | Details: Citation update