9CV5 | pdb_00009cv5

Crystal structure of the metallo-beta-lactamase VIM-31 with L-captopril

• PDB DOI: https://doi.org/10.2210/pdb9CV5/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-28 Released: 2025-07-02 
• Deposition Author(s): Silwal, S.B., Nix, J.C., Page, R.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Mutation of an active site-adjacent residue in VIM indirectly dictates interactions with and blunts inhibition by D-captopril.

Silwal, S.B., Wamsley, B., Wang, Z., Gung, B.W., Nix, J.C., Page, R.C.

(2025) J Inorg Biochem 271: 112975-112975

• PubMed: 40513263 
• DOI: https://doi.org/10.1016/j.jinorgbio.2025.112975
• Primary Citation Related Structures: 
  9CV1, 9CV2, 9CV3, 9CV4, 9CV5


• PubMed Abstract: 
  

  Activity assays and X-ray crystallographic studies were undertaken to elucidate the inhibitory mechanism of captopril stereoisomers on Verona integron-encoded metallo-β-lactamases, specifically VIM-20, VIM-31, and VIM-15. All three VIM-2-like variants (VIM-20, VIM-31, and VIM-15) and VIM-2 expressed in Escherichia coli exhibited catalytic activity with comparable steady-state kinetic parameters. Among the tested thiol drugs (L- and D-captopril, D,L-thiorphan, and 2,3-dimercaprol), IC ₅₀ analyses indicated that D-captopril and 2,3-dimercaprol were more potent inhibitors against the VIM enzymes examined in this study. Notably, the IC ₅₀ value of D-captopril against VIM-31 was an exception, closely resembling that of L-captopril. To elucidate this exceptional inhibitory potency of D-captopril and its binding mode in the active site of VIM-31, high-resolution crystal structures of VIM-20, VIM-31, and VIM-15 in complex with both L- and D-captopril are reported. These findings will help evaluate whether the identified potent inhibitor D-captopril could be further developed as a pan inhibitor targeting the VIM-family enzymes.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA.
Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Beamline 4.2.2, Berkeley, CA, USA.
Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.23 kDa 
• Atom Count: 1,908 
• Modeled Residue Count: 231 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	243	Enterobacter cloacae	Mutation(s): 0  Gene Names: blaVIM-31 EC: 3.5.2.6
UniProt
Find proteins for I3RJZ3 (Enterobacter cloacae) Explore I3RJZ3  Go to UniProtKB:  I3RJZ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X8Z (Subject of Investigation/LOI)	D [auth A]	L-CAPTOPRIL C9 H15 N O3 S FAKRSMQSSFJEIM-RQJHMYQMSA-N
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.58	α = 90
b = 77.222	β = 90
c = 79.036	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Silwal, S.B., Nix, J.C., Page, R.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	128595

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release