MolNFT v1 · #125395 · protein

Structure of deformed wing virus, a honeybee pathogen

5L7Q · VP1: “Structure of deformed wing virus, a honeybee pathogen”. Electron microscopy, 11 pockets (best druggability 0.64). MolNFT v1 #125395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L7Q
Type: protein
Length: 899 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3
UniProt: L0CTV4, E0YTW0, Q7TG18
Pockets: 11 · best druggability 0.64

Structure

electron microscopy · 3 distinct chains · 13% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	252	12% helix, 25% strand	L0CTV4
B	VP2	protein	250	16% helix, 28% strand	E0YTW0
C	VP3	protein	397	13% helix, 28% strand	Q7TG18

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.64	0.78	61	empty
2	172	0.47	0.76	27	empty
3	57	0.46	0.84	19	empty
4	133	0.46	0.77	19	empty
5	112	0.40	0.76	21	empty

Interfaces

3 interfaces between chains.

A–C · 4781 Å² buried · 66 hydrogen bonds · protein-protein
A–B · 1422 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 1312 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5L7Q · Structure of deformed wing virus, a honeybee pathogen · 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 L0CTV4
Every structure of UniProt E0YTW0
Every structure of UniProt Q7TG18
Elsewhere: RCSB PDB 5L7Q · PDBe 5L7Q · UniProt L0CTV4 · UniProt E0YTW0 · UniProt Q7TG18

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