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Cryoem structure of poliovirus receptor bound to poliovirus type 2

Analyse Cryoem structure of poliovirus receptor bound to poliovirus type 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EPF
Type: protein
Length: 1,050 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poliovirus receptor; Protein VP1; Protein VP2; Protein VP4; Protein VP3
UniProt: P15151, P06210
Ligands: SC4, MYR
Pockets: 9 · best druggability 0.86

Structure

electron microscopy · 5 distinct chains · 8% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Poliovirus receptor	protein	213	0% helix, 33% strand	P15151
1	Protein VP1	protein	272	8% helix, 31% strand	P06210
2	Protein VP2	protein	262	13% helix, 37% strand	P06210
4	Protein VP4	protein	68	19% helix, 13% strand	P06210
3	Protein VP3	protein	235	8% helix, 29% strand	P06210

Ligands and binding sites

SC4 · 1[2-chloro-4-methoxy-phenyl-oxymethyl]-4-[2,6-dichloro-phenyl-oxymethyl]-benzene · ligand · chains 1
MYR · Myristic acid · ligand · chains 4

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.86	0.87	122	SC4
2	563	0.77	0.84	56	empty
3	374	0.73	0.85	47	empty
4	88	0.71	0.94	27	empty
5	616	0.68	0.77	53	empty

Interfaces

9 interfaces between chains.

1–2 · 2369 Å² buried · 38 hydrogen bonds · protein-protein
1–3 · 1523 Å² buried · 22 hydrogen bonds · protein-protein
1–4 · 978 Å² buried · 10 hydrogen bonds · protein-protein
R–1 · 962 Å² buried · 16 hydrogen bonds · protein-protein
2–3 · 825 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 lipid (disulfide, myristoylation).

Compared structures

3EPF · CryoEM structure of poliovirus receptor bound to poliovirus type 2 · the same entry in another collection · chain R against R, TM-score 1.00
P15151 · AlphaFold monomer V2.0 prediction for poliovirus receptor (P15151) · a predicted model of the same protein · chain R against A, TM-score 0.83

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P15151
Every structure of UniProt P06210
Elsewhere: RCSB PDB 3EPF · PDBe 3EPF · UniProt P15151 · UniProt P06210

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