MolNFT v1 · #122433 · protein

Tomato spotted wilt tospovirus nucleocapsid protein

5IP1 · Nucleoprotein: “Tomato spotted wilt tospovirus nucleocapsid protein”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #122433 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IP1
Type: protein
Length: 760 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: F4ZD19
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein	protein	246	59% helix, 4% strand	F4ZD19
B, C	Nucleoprotein	protein	257	57% helix, 3% strand	F4ZD19

Pockets

5 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	528	0.75	0.83	72	empty
2	392	0.65	0.79	51	empty
3	61	0.47	0.84	22	empty
4	120	0.43	0.77	19	empty
5	75	0.43	0.81	20	empty

Interfaces

3 interfaces between chains.

B–C · 2164 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1808 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1792 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

5IP1 · Tomato spotted wilt tospovirus nucleocapsid protein · 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 F4ZD19
Elsewhere: RCSB PDB 5IP1 · PDBe 5IP1 · UniProt F4ZD19

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