3SRX

New Delhi Metallo-beta-Lactamase-1 Complexed with Cd

Structural Biology Knowledgebase: 3SRX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3SRX

Classification: hydrolase

Total Structure Weight: 51351.23

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A, B 237 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Fragment: sequence database residues 37-270
Mutation: Q37N, Q38Y
Gene Name(s): blaNDM-1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CD
Query on CD

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

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

B THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.175
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 108.94 α = 90.00
b = 108.94 β = 90.00
c = 237.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-07-07
  • Released Date: 2011-07-20
  • Deposition author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Binkowski, T.A., Mire, J., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MT

Revision History

No revisions since initial release