1KR3

Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.

Structural Biology Knowledgebase: 1KR3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.152

Literature

Macromolecules
Sequence Display for 1KR3

Classification: HYDROLASE

Total Structure Weight: 51669.64

Macromolecule Entities
Molecule Chains Length Organism Details
beta-Lactamase, type II A, B 232 Bacteroides fragilis EC#: 3.5.2.6 IUBMB
Gene Name(s): ccrA cfiA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
113
Query on 113

A, B 7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10- DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID
C15 H14 O8
RSFJMLCZHPZXCW-AANKLQPISA-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)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
113 N/A in BindingDB
Ki: 10000 nM  BindingMOAD
Ki: 10000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.152
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 41.80 α = 92.80
b = 44.20 β = 95.30
c = 58.50 γ = 98.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-08
  • Released Date: 2003-01-08
  • Deposition author(s): Payne, D.J., Hueso-Rodrguez, J.A., Boyd, H., Concha, N.O., Janson, C.A., Gilpin, M., Bateson, J.H., Cheever, C., Niconovich, N.L., Pearson, S., Rittenhouse, S., Tew, D., Dez, E., Prez, P., de la Fuente, J., Rees, M., Rivera-Sagredo, A.

Revision History

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