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)

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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) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LZ4 (Subject of Investigation/LOI)	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
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Wang, S.Y., Wang, S.Y.

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

Revision History  

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