4RAW

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.161
  • R-Value Work: 0.130

Literature

Macromolecules
Sequence Display for 4RAW

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 52618.25

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A, B 243 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Mutation: M67V
Gene Name(s): blaNDM-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZZ7
Query on ZZ7

A, B (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]- 5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
AMPICILLIN (open form) (Synonym)
C16 H21 N3 O5 S
KDAWOPKDXRJNHV-MPPDQPJWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.161
  • R-Value Work: 0.130
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 39.11 α = 90.00
b = 78.77 β = 90.00
c = 133.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-09-11
  • Released Date: 2014-11-26
  • Deposition author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, G., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MT

Revision History

  • Version 1_0: 2014-11-26

    Type: Initial release