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Cryo-EM structure of a particle coxsackievirus A10 at pH 5.5

Analyse Cryo-EM structure of a particle coxsackievirus A10 at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7C4W
Type: protein
Length: 656 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP2; Capsid protein VP3
UniProt: G0YPI2
Pockets: 8 · best druggability 0.66

Structure

electron microscopy · 3 distinct chains · 9% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	214	4% helix, 31% strand	—
B	Capsid protein VP2	protein	220	12% helix, 32% strand	G0YPI2
C	Capsid protein VP3	protein	222	9% helix, 33% strand	G0YPI2

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.66	0.79	47	empty
2	149	0.52	0.80	24	empty
3	101	0.51	0.83	24	empty
4	65	0.41	0.80	18	empty
5	91	0.33	0.73	14	empty

Interfaces

3 interfaces between chains.

A–C · 3137 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 1579 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1559 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7C4W · Cryo-EM structure of A particle Coxsackievirus A10 at pH 5.5 · 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 G0YPI2
Elsewhere: RCSB PDB 7C4W · PDBe 7C4W · UniProt G0YPI2

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