8Y4K | pdb_00008y4k

Metal Beta-Lactamase VIM-2 in Complex with MBL inhibitor B17

PDB DOI: https://doi.org/10.2210/pdb8Y4K/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: 2.50 Å
R-Value Free:
0.278 (Depositor), 0.286 (DCC)
R-Value Work:
0.199 (Depositor), 0.211 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

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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: 50.05 kDa
Atom Count: 3,524
Modeled Residue Count: 462
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-Beta-Lactamase VIM-2	A, B	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0F7KYQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LXG (Subject of Investigation/LOI) Query on A1LXG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	2-[[(3~{R})-6-(azetidin-3-yloxy)-1,1-bis(oxidanyl)-3~{H}-2,1-benzoxaborol-1-ium-3-yl]methyl]prop-2-enoic acid C₁₄ H₁₇ B N O₆ JUFYVFSDLSYUPR-CYBMUJFWSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor), 0.286 (DCC)
R-Value Work: 0.199 (Depositor), 0.211 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.314	α = 90
b = 62.953	β = 100.8
c = 68.354	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81874291;81502989

Revision History (Full details and data files)

Version 1.0: 2025-02-05
Type: Initial release
Version 1.1: 2025-02-26
Changes: Derived calculations

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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.