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Cryo-EM structure of empty coxsackievirus A10 at pH 7.4

Analyse Cryo-EM structure of empty coxsackievirus A10 at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7C4Y
Type: protein
Length: 639 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: 7 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	207	7% helix, 33% strand	—
B	Capsid protein VP2	protein	213	11% helix, 32% strand	G0YPI2
C	Capsid protein VP3	protein	219	9% helix, 31% strand	G0YPI2

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	366	0.69	0.82	42	empty
2	127	0.51	0.80	24	empty
3	87	0.45	0.80	22	empty
4	173	0.44	0.74	28	empty
5	81	0.37	0.77	17	empty

Interfaces

3 interfaces between chains.

A–C · 2626 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 1580 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1577 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7C4Y · Cryo-EM structure of empty Coxsackievirus A10 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
Every structure of UniProt G0YPI2
Elsewhere: RCSB PDB 7C4Y · PDBe 7C4Y · UniProt G0YPI2

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