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Empty coxsackievirus A9 capsid

Analyse Empty coxsackievirus A9 capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J2J
Type: protein
Length: 712 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein VP1; Protein VP3; Protein VP2
UniProt: P21404
Pockets: 12 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein VP1	protein	222	11% helix, 37% strand	P21404
B	Protein VP3	protein	238	8% helix, 30% strand	P21404
C	Protein VP2	protein	252	11% helix, 37% strand	P21404

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	521	0.79	0.85	65	empty
2	98	0.73	0.95	26	empty
3	57	0.69	0.96	15	empty
4	114	0.57	0.84	22	empty
5	170	0.54	0.80	21	empty

Interfaces

3 interfaces between chains.

A–B · 2964 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 1513 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1208 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3J2J · Empty coxsackievirus A9 capsid · 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 P21404
Elsewhere: RCSB PDB 3J2J · PDBe 3J2J · UniProt P21404

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