8PJM

Metallo beta-lactamase VIM2 with compound AK4

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., Schofield, C.
Funding Organization(s): Engineering and Physical Sciences Research Council, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.182
R-Value Work: 0.153
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Metallo beta-lactamase VIM2 with compound AK4

Kranjc, A., Lucic, A., Schofield, C.

To be published.

Macromolecule Content

Total Structure Weight: 26.28 kDa
Atom Count: 2,024
Modelled Residue Count: 232
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0 Go to UniProtKB: Q9K2N0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZJ5 (Subject of Investigation/LOI) Query on ZJ5 Download Ideal Coordinates CCD File SDF format, chain B [auth AAAA] MOL2 format, chain B [auth AAAA]	B [auth AAAA]	~{N}-[[(3~{R})-1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-3-yl]methyl]methanesulfonamide C₉ H₁₃ B N O₅ S GHGXSIOIQUNTKP-VIFPVBQESA-N		Interactions Focus chain B [auth AAAA] Interactions & Density Focus chain B [auth AAAA]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth AAAA] SDF format, chain D [auth AAAA] SDF format, chain E [auth AAAA] MOL2 format, chain C [auth AAAA] MOL2 format, chain D [auth AAAA] MOL2 format, chain E [auth AAAA]	C [auth AAAA], D [auth AAAA], E [auth AAAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth AAAA] Focus chain D [auth AAAA] Focus chain E [auth AAAA] Interactions & Density Focus chain C [auth AAAA] Focus chain D [auth AAAA] Focus chain E [auth AAAA]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth AAAA] SDF format, chain G [auth AAAA] SDF format, chain H [auth AAAA] MOL2 format, chain F [auth AAAA] MOL2 format, chain G [auth AAAA] MOL2 format, chain H [auth AAAA]	F [auth AAAA], G [auth AAAA], H [auth AAAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth AAAA] Focus chain G [auth AAAA] Focus chain H [auth AAAA] Interactions & Density Focus chain F [auth AAAA] Focus chain G [auth AAAA] Focus chain H [auth AAAA]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth AAAA] MOL2 format, chain I [auth AAAA]	I [auth AAAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth AAAA] Interactions & Density Focus chain I [auth AAAA]