2X71

Structural basis for the interaction of lactivicins with serine beta- lactamases

• PDB DOI: https://doi.org/10.2210/pdb2X71/pdb

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


• Deposited: 2010-02-22 Released: 2010-07-14 
• Deposition Author(s): Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Structural Basis for the Interaction of Lactivicins with Serine Beta-Lactamases.

Brown, T., Charlier, P., Herman, R., Schofield, C.J., Sauvage, E.

(2010) J Med Chem 53: 5890

• PubMed: 20593835 
• DOI: https://doi.org/10.1021/jm100437u
• Primary Citation of Related Structures:  
  2X71


• PubMed Abstract: 
  

  Lactivicin (LTV) is a natural non-beta-lactam antibiotic that inhibits penicillin-binding proteins and serine beta-lactamases. A crystal structure of a BS3-LTV complex reveals that, as for its reaction with PBPs, LTV reacts with the nucleophilic serine and that cycloserine and lactone rings of LTV are opened. This structure, together with reported structures of PBP1b with lactivicins, provides a basis for developing improved lactivicin-based gamma-lactam antibiotics.

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Organizational Affiliation: 

Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.

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: 59.6 kDa 
• Atom Count: 4,328 
• Modelled Residue Count: 510 
• 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 P94458 (Bacillus licheniformis) Explore P94458  Go to UniProtKB:  P94458

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L4C	C [auth A]	(2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID C10 H14 N2 O8 ULEFFWARYSNNRF-NYYVKIQXSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EOH	D [auth A], E [auth A], G [auth B], H [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.652	α = 90
b = 104.089	β = 94.45
c = 62.838	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-11-02
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description