4HKY

New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem

Structural Biology Knowledgebase: 4HKY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HKY

Classification: Hydrolase / Antibiotic

Total Structure Weight: 53613.95

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A, B 243 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Gene Name(s): blaNDM-1

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

A, B (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]- 5-[(2R)-tetrahydrofuran-2-yl]-2,3-dihydro- 1,3-thiazole-4-carboxylic acid
C12 H17 N O6 S
CGJDLFMMMJEANA-DAGMQNCNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FPM
Query on FPM

A, B (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)- oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept- 2-ene-2-carboxylic acid
Faropenem (Synonym)
C12 H15 N O5 S
HGGAKXAHAYOLDJ-FHZUQPTBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

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

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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: 2.0 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.204
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 145.63 α = 90.00
b = 39.32 β = 99.96
c = 75.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-15
  • Released Date: 2013-01-23
  • Deposition author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., 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