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Crystal structure of slow bee paralysis virus at 3.4A resolution

Analyse Crystal structure of slow bee paralysis virus at 3.4A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J96
Type: protein
Length: 902 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; Genome polyprotein
UniProt: A7LM73
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	239	9% helix, 27% strand	A7LM73
B	VP2	protein	252	6% helix, 36% strand	A7LM73
C	Genome polyprotein	protein	411	9% helix, 28% strand	A7LM73

Pockets

13 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	145	0.76	0.93	26	empty
2	638	0.71	0.79	91	empty
3	123	0.49	0.80	22	empty
4	120	0.45	0.77	18	empty
5	83	0.45	0.80	22	empty

Interfaces

3 interfaces between chains.

A–C · 4943 Å² buried · 60 hydrogen bonds · protein-protein
A–B · 1595 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1429 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5J96 · Crystal structure of Slow Bee Paralysis Virus at 3.4A 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 5J96 · PDBe 5J96 · UniProt A7LM73

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