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Crystal structure of VP5 from haloarchaeal pleomorphic virus 6

Analyse Crystal structure of VP5 from haloarchaeal pleomorphic virus 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QGL
Type: protein
Length: 720 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP5
UniProt: H9ABP6
Ligands: BR
Pockets: 9 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP5	protein	491	35% helix, 23% strand	H9ABP6
B	VP5	protein	229	56% helix, 15% strand	H9ABP6

Ligands and binding sites

BR · Bromide ion · ion · 25 copies · chains A, B

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

Pockets

9 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	149	0.52	0.80	21	empty
2	170	0.51	0.78	26	empty
3	103	0.45	0.78	18	empty
4	150	0.44	0.75	29	empty
5	77	0.41	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 946 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6QGL · Crystal structure of VP5 from Haloarchaeal pleomorphic virus 6 · 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 H9ABP6
Elsewhere: RCSB PDB 6QGL · PDBe 6QGL · UniProt H9ABP6

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