MolNFT v1 · #62768 · protein

Cryoem structure of poliovirus receptor bound to poliovirus type 1

3EPC: “Cryoem structure of poliovirus receptor bound to poliovirus type 1”. Electron microscopy, 2 ligands (SPH, MYR), 10 pockets (best druggability 0.85). MolNFT v1 #62768 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EPC
Type: protein
Length: 1,061 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, P03300
Ligands: SPH, MYR
Pockets: 10 · best druggability 0.85

Structure

electron microscopy · 5 distinct chains · 9% 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	283	10% helix, 29% strand	P03300
2	Protein VP2	protein	268	13% helix, 38% strand	P03300
4	Protein VP4	protein	62	11% helix, 16% strand	P03300
3	Protein VP3	protein	235	10% helix, 29% strand	P03300

Ligands and binding sites

SPH · Sphingosine · 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

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	960	0.85	0.87	108	empty
2	1119	0.83	0.83	129	SPH
3	77	0.70	0.95	27	empty
4	648	0.69	0.77	67	empty
5	341	0.63	0.79	43	empty

Interfaces

9 interfaces between chains.

1–2 · 2451 Å² buried · 40 hydrogen bonds · protein-protein
1–3 · 1626 Å² buried · 24 hydrogen bonds · protein-protein
1–4 · 1207 Å² buried · 17 hydrogen bonds · protein-protein
R–1 · 919 Å² buried · 14 hydrogen bonds · protein-protein
2–3 · 844 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3EPC · CryoEM structure of poliovirus receptor bound to poliovirus type 1 · 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 0.81

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 P03300
Elsewhere: RCSB PDB 3EPC · PDBe 3EPC · UniProt P15151 · UniProt P03300

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.