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Cryo-EM structure of CVA10 empty particle

Analyse Cryo-EM structure of CVA10 empty particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AKU
Type: protein
Length: 635 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3
UniProt: W0G0K3, A0A0C5AZ80, A0A0C5AWF6
Pockets: 8 · best druggability 0.68

Structure

electron microscopy · 3 distinct chains · 10% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	205	8% helix, 38% strand	W0G0K3
B	VP2	protein	201	10% helix, 37% strand	A0A0C5AZ80
C	VP3	protein	229	10% helix, 31% strand	A0A0C5AWF6

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.68	0.96	16	empty
2	267	0.59	0.79	36	empty
3	158	0.53	0.80	23	empty
4	131	0.53	0.81	21	empty
5	92	0.47	0.81	23	empty

Interfaces

3 interfaces between chains.

A–C · 2733 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 1589 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1343 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6AKU · Cryo-EM structure of CVA10 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 W0G0K3
Every structure of UniProt A0A0C5AZ80
Every structure of UniProt A0A0C5AWF6
Elsewhere: RCSB PDB 6AKU · PDBe 6AKU · UniProt W0G0K3 · UniProt A0A0C5AZ80 · UniProt A0A0C5AWF6

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