Research workbench

Crystallographic structure of full particle of deformed wing virus

Analyse Crystallographic structure of full particle of deformed wing virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G52
Type: protein
Length: 890 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3
Ligands: U5P
Pockets: 9 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	243	5% helix, 22% strand	—
B	VP2	protein	250	12% helix, 23% strand	—
C	VP3	protein	397	10% helix, 26% strand	—

Ligands and binding sites

U5P · Uridine-5'-monophosphate · ligand · chains C

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	468	0.64	0.77	35	empty
2	218	0.54	0.78	27	empty
3	180	0.47	0.75	30	empty
4	157	0.44	0.75	31	empty
5	93	0.41	0.76	15	empty

Interfaces

3 interfaces between chains.

A–C · 4958 Å² buried · 58 hydrogen bonds · protein-protein
A–B · 1491 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1422 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5G52 · Crystallographic structure of full particle of Deformed Wing 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
Elsewhere: RCSB PDB 5G52 · PDBe 5G52

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