2GFJ

Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas maltophilia (inhibitor 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia.

Nauton, L.Kahn, R.Garau, G.Hernandez, J.F.Dideberg, O.

(2008) J Mol Biol 375: 257-269

  • DOI: https://doi.org/10.1016/j.jmb.2007.10.036
  • Primary Citation of Related Structures:  
    2FM6, 2FU7, 2FU8, 2FU9, 2GFJ, 2GFK, 2H6A, 2HB9

  • PubMed Abstract: 
  • One mechanism by which bacteria can escape the action of beta-lactam antibiotics is the production of metallo-beta-lactamases. Inhibition of these enzymes should restore the action of these widely used antibiotics. The tetrameric enzyme L1 from Stenotrophomonas maltophilia was used as a model system to determine a series of high-resolution crystal structures of apo, mono and bi-metal substituted proteins as well as protein-inhibitor complexes ...

    One mechanism by which bacteria can escape the action of beta-lactam antibiotics is the production of metallo-beta-lactamases. Inhibition of these enzymes should restore the action of these widely used antibiotics. The tetrameric enzyme L1 from Stenotrophomonas maltophilia was used as a model system to determine a series of high-resolution crystal structures of apo, mono and bi-metal substituted proteins as well as protein-inhibitor complexes. Unexpectedly, although the apo structure revealed only few significant structural differences from the holo structure, some inhibitors were shown to induce amino acid side-chain rotations in the tightly packed active site. Moreover, one inhibitor employs a new binding mode in order to interact with the di-zinc center. This structural information could prove essential in the process of elucidation of the mode of interaction between a putative lead compound and metallo-beta-lactamases, one of the main steps in structure-based drug design.


    Related Citations: 
    • Update of the standard numbering scheme for class B beta-lactamases
      Garau, G., Garcia-Saez, I., Bebrone, C., Anne, C., Mercuri, P., Galleni, M., Frere, J.M., Dideberg, O.
      (2004) Antimicrob Agents Chemother 48: 2347
    • The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold
      Carfi, A., Pares, S., Duee, E., Galleni, M., Duez, C., Frere, J.M., Dideberg, O.
      (1995) EMBO J 14: 4914

    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel (UMR 5075;CNRS;CEA;UJF), 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallo-beta-lactamase L1
A, B
269Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: L1
EC: 3.5.2.6
UniProt
Find proteins for P52700 (Stenotrophomonas maltophilia)
Explore P52700 
Go to UniProtKB:  P52700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52700
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VI
Query on VI

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
1,3-DIPHENYL-1H-PYRAZOLE-4,5-DICARBOXYLIC ACID
C17 H12 N2 O4
WERNQSNSNVDBBJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
VI Binding MOAD:  2GFJ IC50: 1.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.88α = 90
b = 105.88β = 90
c = 197.86γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
SCALAdata scaling
CCP4model building
REFMACrefinement
XDSdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description