4EYF

Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 4EYF

Classification: Hydrolase / antibiotic

Total Structure Weight: 58152.12

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A, B 270 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
PNK
Query on PNK

A, B (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}- 5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
Penicillin, hydroxylated form (Synonym)
C16 H20 N2 O5 S
HCYWNSXLUZRKJX-RWMBFGLXSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.163
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 39.03 α = 90.00
b = 79.49 β = 90.00
c = 134.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-01
  • Released Date: 2012-08-08
  • Deposition author(s): Strynadka, N.C.J., King, D.T.

Revision History

No revisions since initial release