5N4S | pdb_00005n4s

VIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-methylpropanoyl)-D-tryptophan (Compound 3)

• PDB DOI: https://doi.org/10.2210/pdb5N4S/pdb

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


• Deposited: 2017-02-11 Released: 2017-05-17 
• Deposition Author(s): Li, G.-B., Brem, J., McDonough, M.A., Schofield, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.200 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.185 (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.

---

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: 50.67 kDa 
• Atom Count: 4,094 
• Modeled Residue Count: 463 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase VIM-2	A, B	232	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, PAERUG_P32_London_17_VIM_2_10_11_06255 EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0  Go to UniProtKB:  Q9K2N0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R38	F [auth A], L [auth B]	(2~{R})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid C15 H18 N2 O3 S ZOUTYVWHWSUKPL-NOZJJQNGSA-N
ZN	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
R38	BindingDB:  5N4S	IC50: 526 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.200 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.845	α = 90
b = 80.308	β = 130.34
c = 68.732	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
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: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description