2Y91

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

Structural Biology Knowledgebase: 2Y91 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 2Y91

Classification: HYDROLASE

Total Structure Weight: 59903.85

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-LACTAMASE A, B 265 Bacillus licheniformis EC#: 3.5.2.6 IUBMB
Gene Name(s): penP blaP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
98J
Query on 98J

A, B 5-HYDROXY-3-OXOPENTANOIC ACID
C5 H8 O4
ANTBRXMMNBUYMS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CIT Ki: 490000 nM (97) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
1X6
Query on 1X6
A, B L-PEPTIDE LINKING C6 H10 N2 O4 SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.179
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.79 α = 90.00
b = 103.79 β = 94.82
c = 63.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-11
  • Released Date: 2012-02-22
  • Deposition author(s): Power, P., Sauvage, E., Herman, R., Kerff, F., Charlier, P.

Revision History

  • 2012-09-26
    Type: Citation | Details: JRNL