9L7F | pdb_00009l7f

Metallo Beta-Lactamase VIM-2 in complex with Dual MBL/SBL inhibitor B34

PDB DOI: https://doi.org/10.2210/pdb9L7F/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli BL21(DE3)
Expression System: Klebsiella pneumoniae
Mutation(s): No

Deposited: 2024-12-27 Released: 2025-12-31
Deposition Author(s): Li, G.-B., Liang, G.-Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.194 (Depositor), 0.193 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A class of novel, potent,dual-acting benzoquinte-borate Beta-lactamase inhibitors targeting SBL/MBL

Li, G.-B., Liang, G.-Q.

To be published.

Macromolecule Content

Total Structure Weight: 50.48 kDa
Atom Count: 3,627
Modeled Residue Count: 464
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase VIM-2	A, B	232	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: VIM-2, blaVIM-2, VIM2 EC: 3.5.2.6
UniProt
Find proteins for Q5U7L7 (Escherichia coli) Explore Q5U7L7 Go to UniProtKB: Q5U7L7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5U7L7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EJI (Subject of Investigation/LOI) Query on A1EJI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	(3~{R})-3-[(9~{R})-7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-9-yl]-2-methylidene-butanoic acid C₁₂ H₁₄ B O₅ UMWWMWYMIMKAJG-RDDDGLTNSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]