2Y91

Crystal structure of class A beta-lactamase from Bacillus licheniformis BS3 with clavulanic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel Fragments of Clavulanate Observed in the Structure of the Class a Beta-Lactamase from Bacillus Licheniformis Bs3.

Power, P.Mercuri, P.Herman, R.Kerff, F.Gutkind, G.Dive, G.Galleni, M.Charlier, P.Sauvage, E.

(2012) J.Antimicrob.Chemother. 67: 2379


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE
A, B
265Bacillus licheniformisMutation(s): 0 
Gene Names: penP (blaP)
EC: 3.5.2.6
Find proteins for P00808 (Bacillus licheniformis)
Go to UniProtKB:  P00808
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
98J
Query on 98J

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Download CCD File 
A, B
5-HYDROXY-3-OXOPENTANOIC ACID
C5 H8 O4
ANTBRXMMNBUYMS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
1X6
Query on 1X6
A, B
L-PEPTIDE LINKINGC6 H10 N2 O4SER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CITKi: 490000 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.788α = 90.00
b = 103.790β = 94.82
c = 63.647γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references