4GYU

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae

Structural Biology Knowledgebase: 4GYU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.152

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GYU

Classification: HYDROLASE

Total Structure Weight: 26505.01

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A 243 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Mutation: A121F
Gene Name(s): blaNDM-1

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

A GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
JSmol
P6G
Query on P6G

A HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.152
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.47 α = 90.00
b = 101.47 β = 90.00
c = 42.68 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-05
  • Released Date: 2012-09-26
  • 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