5N0I

Crystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.147
  • R-Value Work: 0.110

Literature

Macromolecules
Sequence Display for 5N0I

Classification: HYDROLASE

Total Structure Weight: 52672.18

Macromolecule Entities
Molecule Chains Length Organism Details
Metallo-beta-lactamase type 2 A, B 244 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Fragment: UNP Residues 29-270
Gene Name(s): blaNDM-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PG4
Query on PG4

B TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-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

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: 1.47 Å
  • R-Value Free: 0.147
  • R-Value Work: 0.110
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 107.22 α = 90.00
b = 107.22 β = 90.00
c = 92.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-03
  • Released Date: 2017-04-05
  • Deposition author(s): Raczynska, J.E., Shabalin, I.G., Jaskolski, M., Minor, W., Wlodawer, A., King, D.T., Strynadka, N.C.J.

Revision History

No revisions since initial release