4RAM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.143

Literature

Macromolecules
Sequence Display for 4RAM

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 52573.28

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
PNM
Query on PNM

A, B OPEN FORM - PENICILLIN G
C16 H20 N2 O4 S
OGFZUTGOGYUTKZ-KWCYVHTRSA-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)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.143
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 39.06 α = 90.00
b = 79.21 β = 90.00
c = 133.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-09-10
  • Released Date: 2014-09-24
  • 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: 2014-09-24

    Type: Initial release