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Cryo-EM structure of CVA6 vlp

Analyse Cryo-EM structure of CVA6 vlp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YHQ
Type: protein
Length: 682 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP3; Capsid protein VP0
UniProt: Q9YLP0, Q6JKS2
Pockets: 11 · best druggability 0.73

Structure

electron microscopy · 3 distinct chains · 10% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	226	8% helix, 30% strand	Q9YLP0
C	Capsid protein VP3	protein	228	10% helix, 30% strand	Q6JKS2
B	Capsid protein VP0	protein	228	13% helix, 34% strand	Q6JKS2

Pockets

11 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	296	0.73	0.86	49	empty
2	116	0.48	0.80	19	empty
3	137	0.48	0.79	30	empty
4	90	0.44	0.80	20	empty
5	112	0.37	0.74	16	empty

Interfaces

3 interfaces between chains.

A–C · 2893 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1817 Å² buried · 28 hydrogen bonds · protein-protein
C–B · 1653 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5YHQ · Cryo-EM Structure of CVA6 VLP · 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
Every structure of UniProt Q9YLP0
Every structure of UniProt Q6JKS2
Elsewhere: RCSB PDB 5YHQ · PDBe 5YHQ · UniProt Q9YLP0 · UniProt Q6JKS2

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