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Cryo-EM structure of CV-A10 native empty particle

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

PDB: 6IIO
Type: protein
Length: 670 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.12
Source: Coxsackievirus A10
Molecule: VP1; VP0; VP3
UniProt: A0A1B3Z4Y8
Pockets: 11 · best druggability 0.74

Structure

electron microscopy · resolution 3.12 · 3 distinct chains · 11% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	221	10% helix, 31% strand	A0A1B3Z4Y8
B	VP0	protein	216	13% helix, 35% strand	A0A1B3Z4Y8
C	VP3	protein	233	11% helix, 35% strand	A0A1B3Z4Y8

Pockets

11 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	256	0.74	0.88	45	empty
2	137	0.53	0.81	27	empty
3	58	0.49	0.85	20	empty
4	122	0.45	0.78	26	empty
5	121	0.44	0.77	25	empty

Interfaces

3 interfaces between chains.

A–C · 3006 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 1770 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1583 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6IIO · Cryo-EM structure of cv-A10 native empty particle · 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 A0A1B3Z4Y8
Elsewhere: RCSB PDB 6IIO · PDBe 6IIO · UniProt A0A1B3Z4Y8

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