1M2X

Crystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum in complex with the inhibitor D-captopril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.190 

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This is version 1.3 of the entry. See complete history


Literature

The 1.5 A structure of Chryseobacterium meningosepticum Zn-beta-lactamase in complex with the inhibitor, D-captopril

Garcia-Saez, I.Hopkins, J.Papamicael, C.Franceschini, N.Amicosante, G.Rossolini, G.M.Galleni, M.Frere, J.M.Dideberg, O.

(2003) J Biol Chem 278: 23868-23873

  • DOI: https://doi.org/10.1074/jbc.M301062200
  • Primary Citation of Related Structures:  
    1M2X

  • PubMed Abstract: 

    The crystal structure of the class-B beta-lactamase, BlaB, from the pathogenic bacterium, Chryseobacterium meningosepticum, in complex with the inhibitor, d-captopril, has been solved at 1.5-A resolution. The enzyme has the typical alphabeta/betaalpha metallo-beta-lactamase fold and the characteristic two metal binding sites of members of the subclass B1, in which two Zn2+ ions were identified. d-Captopril, a diastereoisomer of the commercial drug, captopril, acts as an inhibitor by displacing the catalytic hydroxyl ion required for antibiotic hydrolysis and intercalating its sulfhydryl group between the two Zn2+ ions. Interestingly, d-captopril is located on one side of the active site cleft. The x-ray structure of the complex of the closely related enzyme, IMP-1, with a mercaptocarboxylate inhibitor, which also contains a sulfhydryl group bound to the two Zn2+ ions, shows the ligand to be located on the opposite side of the active site cleft. A molecule generated by fusion of these two inhibitors would cover the entire cleft, suggesting an interesting approach to the design of highly specific inhibitors.


  • Organizational Affiliation

    Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CNRS-Commissariat à l'Energie Atomique, Saclay, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
class B carbapenemase BlaB-1
A, B, C, D
223Elizabethkingia meningosepticaMutation(s): 0 
Gene Names: blaB
EC: 3.5.2.6
UniProt
Find proteins for O08498 (Elizabethkingia meningoseptica)
Explore O08498 
Go to UniProtKB:  O08498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08498
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MCO
Query on MCO

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
S [auth C],
X [auth D]
1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
C9 H15 N O3 S
FAKRSMQSSFJEIM-RNFRBKRXSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
T [auth C],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
R [auth C],
U [auth D],
V [auth D],
W [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MCO Binding MOAD:  1M2X Ki: 8.50e+4 (nM) from 1 assay(s)
PDBBind:  1M2X Ki: 7.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.190 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.685α = 90
b = 159.685β = 90
c = 97.815γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description