2Y91

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

• PDB DOI: https://doi.org/10.2210/pdb2Y91/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.219 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

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

• PubMed: 22773738 
• DOI: https://doi.org/10.1093/jac/dks231
• Primary Citation of Related Structures:  
  2Y91


• PubMed Abstract: 
  

  Our aim was to unravel the inactivation pathway of the class A β-lactamase produced by Bacillus licheniformis BS3 (BS3) by clavulanate.

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Organizational Affiliation: 

Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 956, (1113) Buenos Aires, Argentina.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.9 kDa 
• Atom Count: 4,336 
• Modelled Residue Count: 514 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE	A, B	265	Bacillus licheniformis	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808  Go to UniProtKB:  P00808

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
98J	C [auth A], F [auth B], G [auth B]	5-HYDROXY-3-OXOPENTANOIC ACID C5 H8 O4 ANTBRXMMNBUYMS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1X6	A, B	L-PEPTIDE LINKING	C6 H10 N2 O4		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
CIT	BindingDB:  2Y91	Ki: 4.90e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.219 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.788	α = 90
b = 103.79	β = 94.82
c = 63.647	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description