6T48 | pdb_00006t48

Bovine enterovirus F3 in complex with glutathione and a Cysteinylglycine dipeptide

PDB DOI: https://doi.org/10.2210/pdb6T48/pdb

Classification: VIRUS
Organism(s): Enterovirus F
Mutation(s): No

Deposited: 2019-10-12 Released: 2020-01-15
Deposition Author(s): Duyvesteyn, H.M.E., Ren, J., Walter, T.S., Fry, E.E., Stuart, D.I.
Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.203 (Depositor), 0.196 (DCC)
R-Value Work:
0.200 (Depositor), 0.196 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Glutathione facilitates enterovirus assembly by binding at a druggable pocket.

Duyvesteyn, H.M.E., Ren, J., Walter, T.S., Fry, E.E., Stuart, D.I.

(2020) Commun Biol 3: 9-9

PubMed: 31909201 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-019-0722-x
Primary Citation Related Structures:
6T40, 6T48, 6T4C

PubMed Abstract:
Enteroviruses cause a range of human and animal diseases, some life-threatening, but there remain no licenced anti-enterovirus drugs. However, a benzene-sulfonamide derivative and related compounds have been shown recently to block infection of a range of enteroviruses by binding the capsid at a positively-charged surface depression conserved across many enteroviruses. It has also been established that glutathione is essential for the assembly of many enteroviruses, interacting with the capsid proteins to facilitate the formation of the pentameric assembly intermediate, although the mechanism is unknown. Here we show, by high resolution structure analyses of enterovirus F3, that reduced glutathione binds to the same interprotomer pocket as the benzene-sulfonamide derivative. Bound glutathione makes strong interactions with adjacent protomers, thereby explaining the underlying biological role of this druggable binding pocket and delineating the pharmacophore for potential antivirals.

Organizational Affiliation

1Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK.

Macromolecule Content

Total Structure Weight: 93.54 kDa
Atom Count: 6,992
Modeled Residue Count: 806
Deposited Residue Count: 833
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	275	Enterovirus F	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q2LKZ0 (Enterovirus F) Explore Q2LKZ0 Go to UniProtKB: Q2LKZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2LKZ0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	244	Enterovirus F	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q2LKZ0 (Enterovirus F) Explore Q2LKZ0 Go to UniProtKB: Q2LKZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2LKZ0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	243	Enterovirus F	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q2LKZ0 (Enterovirus F) Explore Q2LKZ0 Go to UniProtKB: Q2LKZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2LKZ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	D	71	Enterovirus F	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q2LKZ0 (Enterovirus F) Explore Q2LKZ0 Go to UniProtKB: Q2LKZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2LKZ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH (Subject of Investigation/LOI) Query on GSH Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
STE Query on STE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CYS Query on CYS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], N [auth B], Q [auth C], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth C] SDF format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B]	L [auth A], M [auth A], O [auth B], S [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain S [auth C] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain S [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	T [auth C], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain T [auth C] Focus chain U [auth C]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	G [auth A]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]