3RKK

Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae

Structural Biology Knowledgebase: 3RKK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 3RKK

Classification: HYDROLASE

Total Structure Weight: 51389.60

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 39-270
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
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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)
ACY
Query on ACY

B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 59.76 α = 90.00
b = 50.86 β = 106.98
c = 70.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-18
  • Released Date: 2011-05-18
  • Deposition author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Binkowski, T.A., 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

  • 2012-03-28
    Type: Citation | Details: Citation update
  • 2011-09-21
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4