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Crystal structure of helicoverpa armigera stunt virus

Analyse Crystal structure of helicoverpa armigera stunt virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S6P
Type: protein
Length: 2,319 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: Q82462
Ligands: CA, CL
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 8 distinct chains · 21% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	529	18% helix, 37% strand	Q82462
E	Capsid protein	protein	33	88% helix, 0% strand	Q82462
B	Capsid protein	protein	530	18% helix, 37% strand	Q82462
F	Capsid protein	protein	24	83% helix, 0% strand	Q82462
C	Capsid protein	protein	536	18% helix, 37% strand	Q82462
G	Capsid protein	protein	72	49% helix, 6% strand	Q82462
D	Capsid protein	protein	532	17% helix, 38% strand	Q82462
H	Capsid protein	protein	63	51% helix, 0% strand	Q82462

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B, C
CL · Chloride ion · ion · 2 copies · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.88	0.91	134	empty
2	810	0.86	0.89	64	CA
3	791	0.84	0.87	90	CL
4	370	0.84	0.93	35	empty
5	788	0.79	0.83	89	empty

Interfaces

16 interfaces between chains.

B–C · 2765 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 2450 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 2387 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 2004 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 1586 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3S6P · Crystal Structure of Helicoverpa Armigera Stunt Virus · 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 Q82462
Elsewhere: RCSB PDB 3S6P · PDBe 3S6P · UniProt Q82462

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