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Cryo electron microscopy structure of grapevine fanleaf virus complex with nanobody

Analyse Cryo electron microscopy structure of grapevine fanleaf virus complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FOJ
Type: protein
Length: 634 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nanobody; RNA2 polyprotein
UniProt: P18474
Pockets: 13 · best druggability 0.77

Structure

electron microscopy · 2 distinct chains · 7% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nanobody	protein	130	2% helix, 32% strand	—
B	RNA2 polyprotein	protein	504	8% helix, 38% strand	P18474

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.77	0.98	17	empty
2	244	0.71	0.86	44	empty
3	279	0.65	0.82	37	empty
4	102	0.61	0.87	22	empty
5	197	0.52	0.78	24	empty

Interfaces

1 interface between chains.

A–B · 863 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5FOJ · Cryo electron microscopy structure of Grapevine Fanleaf Virus complex with Nanobody · 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 P18474
Elsewhere: RCSB PDB 5FOJ · PDBe 5FOJ · UniProt P18474

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