MolNFT v1 · #152552 · protein

Cryo-EM structure of empty echovirus 6 particle at pH 7.4

6ILO · Capsid protein VP1: “Cryo-EM structure of empty echovirus 6 particle at pH 7.4”. Electron microscopy, 9 pockets (best druggability 0.64). MolNFT v1 #152552 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ILO
Type: protein
Length: 693 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP2; Capsid protein VP3
Pockets: 9 · best druggability 0.64

Structure

electron microscopy · 3 distinct chains · 8% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	227	7% helix, 34% strand	—
B	Capsid protein VP2	protein	242	7% helix, 33% strand	—
C	Capsid protein VP3	protein	224	9% helix, 30% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.64	0.82	43	empty
2	86	0.45	0.80	22	empty
3	87	0.44	0.80	21	empty
4	59	0.41	0.81	13	empty
5	54	0.40	0.81	17	empty

Interfaces

3 interfaces between chains.

A–C · 3129 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 1763 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1515 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6ILO · Cryo-EM structure of empty Echovirus 6 particle at PH 7.4 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6ILO · PDBe 6ILO

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