8Y4M | pdb_00008y4m

Metal Beta-Lactamase VIM-2 in Complex with MBL inhibitor B9

PDB DOI: https://doi.org/10.2210/pdb8Y4M/pdb

Classification: METAL BINDING PROTEIN/INHIBITOR
Organism(s): Enterobacteriaceae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-30 Released: 2025-02-05
Deposition Author(s): Li, G.-B., Wang, S.-Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.314 (Depositor), 0.322 (DCC)
R-Value Work:
0.239 (Depositor), 0.248 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of 2-((1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)methyl)acrylic acids as potent MBL inhibitors

Liang, G.-Q., Wang, S.-Y., Li, G.-B.

To be published.

Macromolecule Content

Total Structure Weight: 75.07 kDa
Atom Count: 5,321
Modeled Residue Count: 693
Deposited Residue Count: 693
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-Beta-Lactamase VIM-2	A, B, C	231	Enterobacteriaceae	Mutation(s): 0 Gene Names: blaVIM2 EC: 3.5.2.6
UniProt
Find proteins for A0A0F7KYQ8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore A0A0F7KYQ8 Go to UniProtKB: A0A0F7KYQ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F7KYQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LXH (Subject of Investigation/LOI) Query on A1LXH Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C]	2-[[(9~{R})-3-(4-methoxyphenoxy)-7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-9-yl]methyl]prop-2-enoic acid C₁₈ H₁₈ B O₇ LKZWSGRMMVRPIY-QGZVFWFLSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] G [auth B] H [auth B] J [auth C] D [auth A], E [auth A], G [auth B], H [auth B], J [auth C], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C]