1KDS

X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid

Structural Biology Knowledgebase: 1KDS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 1KDS

Classification: HYDROLASE

Total Structure Weight: 79510.55

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-LACTAMASE A, B 358 Escherichia coli EC#: 3.5.2.6 IUBMB
Gene Name(s): ampC ampA b4150 JW4111
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NPB
Query on NPB

A, B 3-NITROPHENYLBORONIC ACID
C6 H6 B N O4
ZNRGSYUVFVNSAW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NPB IC50: 5000 nM (100) BindingDB
Ki: 1700 nM (100) BindingDB

N/A in BindingMoad
Ki: 1700 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.174
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.11 α = 90.00
b = 77.73 β = 115.86
c = 99.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-13
  • Released Date: 2002-07-17
  • Deposition author(s): Powers, R.A., Shoichet, B.K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4