1Y54 | pdb_00001y54

Crystal structure of the native class C beta-lactamase from Enterobacter cloacae 908R complexed with BRL42715

• PDB DOI: https://doi.org/10.2210/pdb1Y54/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-02 Released: 2005-03-29 
• Deposition Author(s): Michaux, C., Charlier, P., Frere, J.-M., Wouters, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.292 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal Structure of BRL 42715, C6-(N1-Methyl-1,2,3-triazolylmethylene)penem, in Complex with Enterobactercloacae 908R beta-Lactamase: Evidence for a Stereoselective Mechanism from Docking Studies

Michaux, C., Charlier, P., Frere, J.-M., Wouters, J.

(2005) J Am Chem Soc 127: 3262-3263

• PubMed: 15755127 
• DOI: https://doi.org/10.1021/ja0426241
• Primary Citation Related Structures: 
  1Y54


• PubMed Abstract: 
  

  BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, is an active-site-directed inactivator of bacterial beta-lactamases. The crystal structure of Enterobacter cloacae 908R class C beta-lactamase in complex with BRL 42715, docking, and energy minimization studies explain stereoselectivity of the binding of C6-(heterocyclic methylene)penems against class C beta-lactamase.

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Organizational Affiliation: 
• Laboratoire de Chimie Biologique Structurale, Université of Namur, 5000 Namur, Belgium.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.58 kDa 
• Atom Count: 2,916 
• Modeled Residue Count: 359 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	361	Enterobacter cloacae	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for P05364 (Enterobacter cloacae) Explore P05364  Go to UniProtKB:  P05364

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDT	B [auth A]	(7R)-6-FORMYL-7-(1-METHYL-1H-1,2,3-TRIAZOL-4-YL)-4,7-DIHYDRO-1,4-THIAZEPINE-3-CARBOXYLIC ACID C10 H10 N4 O3 S BCPHJDLBOJMWOD-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.292 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.365	α = 90
b = 82.221	β = 90
c = 96.156	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
CCP4	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-29 
Deposition Author(s): Michaux, C., Charlier, P., Frere, J.-M., Wouters, J.

Revision History  

• Version 1.0: 2005-03-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2024-11-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary