6Y6J | pdb_00006y6j

VIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products

PDB DOI: https://doi.org/10.2210/pdb6Y6J/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-26 Released: 2021-03-31
Deposition Author(s): Lucic, A., Schofield, C.J., Brem, J., McDonough, M.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.157 (Depositor), 0.165 (DCC)
R-Value Work:
0.129 (Depositor), 0.142 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of metallo-beta-lactamase VIM-2 in complex with the imine and enamine form of hydrolysed Biapenem

Lucic, A., Saward, B.G., Brem, J., McDonough, M.A., Calvopina, K., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 25.81 kDa
Atom Count: 2,048
Modeled Residue Count: 232
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase VIM-2	A	232	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaVIM-2 EC: 3.5.2.6
UniProt
Find proteins for D1MEN9 (Pseudomonas aeruginosa) Explore D1MEN9 Go to UniProtKB: D1MEN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1MEN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OEN (Subject of Investigation/LOI) Query on OEN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Biapenem Imine hydrolysis product C₁₅ H₂₁ N₄ O₅ S FWQUIKBOZBJCAG-PAMYDDKSSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
OEQ (Subject of Investigation/LOI) Query on OEQ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Biapenem Enamine hydrolysis product C₁₅ H₂₁ N₄ O₅ S NNMZLHRXLIBHJJ-YJFSRANCSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]