1S6R | pdb_00001s6r

908R class c beta-lactamase bound to iodo-acetamido-phenyl boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.293 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.239 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1S6R

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Enterobacter cloacae 908R class C beta-lactamase bound to iodo-acetamido-phenyl boronic acid, a transition-state analogue.

Wouters, J.Fonze, E.Vermeire, M.Frere, J.M.Charlier, P.

(2003) Cell Mol Life Sci 60: 1764-1773

  • DOI: https://doi.org/10.1007/s00018-003-3189-2
  • Primary Citation Related Structures: 
    1S6R

  • PubMed Abstract: 

    The structures of the class C beta-lactamase from Enterobacter cloacae 908R alone and in complex with a boronic acid transition-state analogue were determined by X-ray crystallography at 2.1 and 2.3 A, respectively. The structure of the enzyme resembles those of other class C beta-lactamases. The structure of the complex with the transition-state analogue, iodo-acetamido-phenyl boronic acid, shows that the inhibitor is covalently bound to the active-site serine (Ser64). Binding of the inhibitor within the active site is compared with previously determined structures of complexes with other class C enzymes. The structure of the boronic acid adduct indicates ways to improve the affinity of this class of inhibitors. This structure of 908R class C beta-lactamase in complex with a transition-state analogue provides further insights into the mechanism of action of these hydrolases.


  • Organizational Affiliation
    • Institut de Recherche Microbiologiques JM Wiame, Brussels, Belgium. jwouters@dbm.ulb.ac.be

Macromolecule Content 

  • Total Structure Weight: 39.4 kDa 
  • Atom Count: 2,817 
  • Modeled Residue Count: 359 
  • Deposited Residue Count: 359 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
beta-lactamase359Enterobacter cloacaeMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for Q93CA2 (Enterobacter cloacae)
Explore Q93CA2 
Go to UniProtKB:  Q93CA2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93CA2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IAP

Query on IAP



Download:Ideal Coordinates CCD File
B [auth A]4-IODO-ACETAMIDO PHENYLBORONIC ACID
C8 H9 B I N O3
LMHXPDZPXBIIEX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.293 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.239 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.381α = 90
b = 83.763β = 90
c = 95.81γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2004-02-24 
  • Deposition Author(s): Wouters, J.

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary