5N58 | pdb_00005n58

di-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/pdb5N58/pdb

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


• Deposited: 2017-02-13 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: 1.96 Å
• R-Value Free: 
  0.237 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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 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 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.34 kDa 
• Atom Count: 3,498 
• Modeled Residue Count: 441 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class B metallo-beta-lactamase	A, B	266	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaVIM-5 EC: 3.5.2.6
UniProt
Find proteins for Q8GKX2 (Klebsiella pneumoniae) Explore Q8GKX2  Go to UniProtKB:  Q8GKX2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
93W	D [auth A], I [auth B]	(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	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], G [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.237 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.471	α = 90
b = 81.54	β = 90
c = 95.892	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