8YO2 | pdb_00008yo2

Metallo-beta-lactamase VIM-2 in Complex with MBL Inhibitor B4

PDB DOI: https://doi.org/10.2210/pdb8YO2/pdb

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

Deposited: 2024-03-12 Released: 2025-03-19
Deposition Author(s): Wang, S.Y., Wang, S.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.198 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.0 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: 50.33 kDa
Atom Count: 3,764
Modeled Residue Count: 464
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase VIM-2	A, B	232	Enterobacteriaceae	Mutation(s): 0 EC: 3.5.2.6
UniProt
Find proteins for Q5U7L7 (Escherichia coli) Explore Q5U7L7 Go to UniProtKB: Q5U7L7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5U7L7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LZ4 (Subject of Investigation/LOI) Query on A1LZ4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	2-[[(3~{R})-6-chloranyl-1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-3-yl]methyl]prop-2-enoic acid C₁₁ H₁₁ B Cl O₅ SGRBFLNXBYZQFQ-SNVBAGLBSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.184 (Depositor), 0.198 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.588	α = 90
b = 79.095	β = 129.97
c = 66.925	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.