5N5I

Crystal Structure of VIM-1 metallo-beta-lactamase in complex with hydrolysed meropenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-beta-lactamases.

Salimraj, R.Hinchliffe, P.Kosmopoulou, M.Tyrrell, J.M.Brem, J.van Berkel, S.S.Verma, A.Owens, R.J.McDonough, M.A.Walsh, T.R.Schofield, C.J.Spencer, J.

(2019) FEBS J. 286: 169-183


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase VIM-1
A
253Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM (blaVIM-1)
Find proteins for Q9XAY4 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q9XAY4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LMP
Query on LMP

Download SDF File 
Download CCD File 
A
(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
Hydrolyzed Meropenem
C17 H27 N3 O6 S
CDYPSIIDXKMBLV-CFINEGTKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.943α = 90.00
b = 68.084β = 90.00
c = 39.817γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N002679/1

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references