4EXS

Crystal structure of NDM-1 bound to L-captopril

Structural Biology Knowledgebase: 4EXS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 4EXS

Classification: Hydrolase / antibiotic

Total Structure Weight: 58175.86

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A, B 272 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Gene Name(s): blaNDM-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
X8Z
Query on X8Z

A, B L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
X8Z N/A in BindingDB
Ki: 39000 nM  BindingMOAD
Ki: 39000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.190
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 107.12 α = 90.00
b = 107.12 β = 90.00
c = 92.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-30
  • Released Date: 2012-08-08
  • Deposition author(s): Strynadka, N.C.J., King, D.T.

Revision History

No revisions since initial release