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Crystal structure of slow bee paralysis virus at 2.6A resolution

Analyse Crystal structure of slow bee paralysis virus at 2.6A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J98
Type: protein
Length: 929 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3
UniProt: A7LM73
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	252	15% helix, 29% strand	A7LM73
B	VP2	protein	260	12% helix, 38% strand	A7LM73
C	VP3	protein	417	11% helix, 32% strand	A7LM73

Pockets

12 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	891	0.74	0.78	75	empty
2	102	0.50	0.81	20	empty
3	191	0.48	0.76	25	empty
4	148	0.47	0.77	23	empty
5	65	0.44	0.82	14	empty

Interfaces

3 interfaces between chains.

A–C · 4776 Å² buried · 78 hydrogen bonds · protein-protein
A–B · 1553 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1447 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5J98 · Crystal structure of Slow Bee Paralysis Virus at 2.6A resolution · 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 A7LM73
Elsewhere: RCSB PDB 5J98 · PDBe 5J98 · UniProt A7LM73

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