8PGM

Crystal structure of the metallo-beta-lactamase VIM1 with 3062


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of the metallo-beta-lactamase VIM1 with 3062

Calvopina, K.Brem, J.Farley, A.J.M.Allen, M.D.Schofield, C.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase VIM-1266Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIMblaVIM-1CAZ10_38240CAZ10_38245
UniProt
Find proteins for Q9XAY4 (Pseudomonas aeruginosa)
Explore Q9XAY4 
Go to UniProtKB:  Q9XAY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XAY4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YU0 (Subject of Investigation/LOI)
Query on YU0

Download Ideal Coordinates CCD File 
D [auth A]3-[4-[(azanyl-methyl-oxidanyl-$l^{4}-sulfanyl)methyl]-3-fluoranyl-phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid
C20 H23 F N2 O3 S
MQEDGVPPDOWGOB-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.42α = 90
b = 67.83β = 93.28
c = 40.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom099141/Z/12/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release