8PJM | pdb_00008pjm

Metallo beta-lactamase VIM2 with compound AK110

• PDB DOI: https://doi.org/10.2210/pdb8PJM/pdb

• Classification: ANTIBIOTIC
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-23 Released: 2023-08-16 
• Deposition Author(s): Lucic, A., Hinchliffe, P., Schofield, C.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.156 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

Metallo beta-lactamase VIM2 with compound AK110

Kranjc, A., Lucic, A., Schofield, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.33 kDa 
• Atom Count: 2,129 
• Modeled Residue Count: 232 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase VIM-2	A [auth AAAA]	242	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, PAERUG_P32_London_17_VIM_2_10_11_06255 EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0  Go to UniProtKB:  Q9K2N0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H7J (Subject of Investigation/LOI)	I [auth AAAA]	~{N}-[[(3~{R})-1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-3-yl]methyl]pyrrolidine-1-sulfonamide C12 H18 B N2 O5 S AQWMHRDFDPGTAN-LBPRGKRZSA-N
ZN	B [auth AAAA], C [auth AAAA], D [auth AAAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth AAAA], F [auth AAAA], G [auth AAAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth AAAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.156 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.653	α = 90
b = 74.086	β = 90
c = 78.739	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Lucic, A., Hinchliffe, P., Schofield, C.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Database references, Structure summary
• Version 2.0: 2024-05-01
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary