MolNFT v1 · #2831 · protein

Tobacco necrosis virus

1C8N · Coat protein: “Tobacco necrosis virus”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.80). MolNFT v1 #2831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1C8N
Type: protein
Length: 597 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coat protein
UniProt: Q9IPS9
Ligands: CA
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coat protein	protein	189	17% helix, 37% strand	Q9IPS9
B	Coat protein	protein	189	19% helix, 37% strand	Q9IPS9
C	Coat protein	protein	219	16% helix, 35% strand	Q9IPS9

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, C, B

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

Pockets

2 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	177	0.80	0.95	43	empty
2	149	0.44	0.76	25	empty

Interfaces

3 interfaces between chains.

B–C · 921 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 883 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1C8N · Tobacco necrosis 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 Q9IPS9
Elsewhere: RCSB PDB 1C8N · PDBe 1C8N · UniProt Q9IPS9

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