3Q6X

Crystal structure of NDM-1 in complex with hydrolyzed ampicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.167
  • R-Value Work: 0.147

Literature

Macromolecules
Sequence Display for 3Q6X

Classification: Hydrolase / Antibiotic

Total Structure Weight: 52526.59

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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZZ7
Query on ZZ7

A, B (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]- 5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
AMPICILLIN (open form) (Synonym)
C16 H21 N3 O5 S
KDAWOPKDXRJNHV-MPPDQPJWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.167
  • R-Value Work: 0.147
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 39.21 α = 90.00
b = 79.10 β = 90.00
c = 134.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-04
  • Released Date: 2011-05-18
  • Deposition author(s): Zhang, H., Hao, Q.

Revision History

  • 2014-03-05
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4