4UA4 | pdb_00004ua4

Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4UA4/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-08 Released: 2014-09-17 
• Deposition Author(s): Spencer, J.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor

Spencer, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 52.73 kDa 
• Atom Count: 4,039 
• Modeled Residue Count: 464 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase class B VIM-2	A, B	242	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0  Go to UniProtKB:  Q9K2N0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3C7	F [auth A], G [auth A], H [auth B]	(3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid C7 H11 N O2 S3 ZTWVMVSSSBGFHH-JKUQZMGJSA-N
GOL	E [auth A], K [auth B], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3C7	BindingDB:  4UA4	Ki: min: 3700, max: 6000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.888	α = 90
b = 61.404	β = 100.87
c = 68.918	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Spencer, J.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	R01AI100560

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description