5NAI

mono-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-D-tryptophan (Compound 1)

• PDB DOI: https://doi.org/10.2210/pdb5NAI/pdb

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


• Deposited: 2017-02-28 Released: 2017-05-17 
• Deposition Author(s): Li, G.-B., Brem, J., McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.141 
• R-Value Work: 0.131 
• R-Value Observed: 0.131 

Starting Model: experimental

Literature

Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-beta-lactamase inhibition.

Li, G.B., Brem, J., Lesniak, R., Abboud, M.I., Lohans, C.T., Clifton, I.J., Yang, S.Y., Jimenez-Castellanos, J.C., Avison, M.B., Spencer, J., McDonough, M.A., Schofield, C.J.

(2017) Chem Commun (Camb) 53: 5806-5809

• PubMed: 28470248 
• DOI: https://doi.org/10.1039/c7cc02394d
• Primary Citation of Related Structures:  
  5N4S, 5N4T, 5N55, 5N58, 5NAI


• PubMed Abstract: 
  

  Crystallographic analyses of the VIM-5 metallo-β-lactamase (MBL) with isoquinoline inhibitors reveal non zinc ion binding modes. Comparison with other MBL-inhibitor structures directed addition of a zinc-binding thiol enabling identification of potent B1 MBL inhibitors. The inhibitors potentiate meropenem activity against clinical isolates harboring MBLs.

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Organizational Affiliation: 

Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.84 kDa 
• Atom Count: 2,101 
• Modelled Residue Count: 232 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class B metallo-beta-lactamase	A	266	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaVIM-5
UniProt
Find proteins for Q8GKX2 (Klebsiella pneumoniae) Explore Q8GKX2  Go to UniProtKB:  Q8GKX2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
93W	E [auth A]	(2~{R})-2-[(1-chloranyl-4-oxidanyl-isoquinolin-3-yl)carbonylamino]-3-(1~{H}-indol-3-yl)propanoic acid C21 H16 Cl N3 O4 PVDFWPDMZYPBMH-MRXNPFEDSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
F	G [auth A], H [auth A]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.141 
• R-Value Work: 0.131 
• R-Value Observed: 0.131 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.553	α = 90
b = 67.555	β = 92.66
c = 40.093	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): Li, G.-B., Brem, J., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description