5N4S

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 ?
R-Value Free: 0.200
R-Value Work: 0.184
R-Value Observed: 0.185

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. christopher.schofield@chem.ox.ac.uk jurgen.brem@chem.ox.ac.uk.

Macromolecule Content

Total Structure Weight: 50.67 kDa
Atom Count: 4,094
Modelled Residue Count: 463
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R38 Query on R38 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	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		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] M [auth B] N [auth B] O [auth B] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 ?
R-Value Free: 0.200
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

5N4S

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)