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Cryoem structure of poliovirus receptor bound to poliovirus

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

PDB: 1NN8
Type: protein
Length: 1,756 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poliovirus receptor; Coat protein VP1; Coat protein VP2; Coat protein VP3; Coat protein…
UniProt: P15151, P03300
Ligands: MYR
Pockets: 5 · best druggability 0.80

Structure

electron microscopy · 5 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R, S, T	Poliovirus receptor	protein	301	0% helix, 0% strand	P15151
1	Coat protein VP1	protein	288	0% helix, 0% strand	P03300
2	Coat protein VP2	protein	268	0% helix, 0% strand	P03300
3	Coat protein VP3	protein	235	0% helix, 0% strand	P03300
4	Coat protein VP4	protein	62	0% helix, 0% strand	P03300

Ligands and binding sites

MYR · Myristic acid · ion · chains 4

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	591	0.80	0.84	189	empty
2	462	0.79	0.85	136	empty
3	201	0.70	0.85	102	empty
4	232	0.64	0.81	72	empty
5	164	0.44	0.72	46	empty

Interfaces

12 interfaces between chains.

S–T · 8118 Å² buried · 0 hydrogen bonds · protein-protein
R–S · 7472 Å² buried · 0 hydrogen bonds · protein-protein
R–T · 7286 Å² buried · 0 hydrogen bonds · protein-protein
1–3 · 558 Å² buried · 0 hydrogen bonds · protein-protein
1–2 · 421 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1NN8 · CryoEM structure of poliovirus receptor bound to poliovirus · the same entry in another collection · chain 4 against 4, 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 0.69

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 1NN8 · PDBe 1NN8 · UniProt P15151 · UniProt P03300

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