Research workbench

Crystal structure of VP9 from white spot syndrome virus

Analyse Crystal structure of VP9 from white spot syndrome virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GJ2
Type: protein
Length: 316 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: WSV230
UniProt: Q91LD0
Ligands: CD
Pockets: 5 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	WSV230	protein	79	16% helix, 33% strand	Q91LD0

Ligands and binding sites

CD · Cadmium ion · metal · 8 copies · chains A, D, B, C

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.47	0.84	20	CD
2	70	0.41	0.80	21	CD
3	79	0.35	0.76	19	CD
4	66	0.33	0.76	18	empty
5	82	0.33	0.75	20	empty

Interfaces

2 interfaces between chains.

A–D · 479 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 468 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2GJ2 · Crystal Structure of VP9 from White Spot Syndrome 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 Q91LD0
Elsewhere: RCSB PDB 2GJ2 · PDBe 2GJ2 · UniProt Q91LD0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.