MolNFT v1 · #140309 · protein

Structure of tomato spotted wilt virus nucleocapsid protein with alternative oligomerization state

5Y6J · Nucleoprotein: “Structure of tomato spotted wilt virus nucleocapsid protein with alternative oligomerization state”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #140309 on GenesisL1: 3D structure, binding sites…

PDB: 5Y6J
Type: protein
Length: 736 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: H6UMW9
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 59% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein	protein	243	60% helix, 2% strand	H6UMW9
B	Nucleoprotein	protein	246	59% helix, 2% strand	H6UMW9
C	Nucleoprotein	protein	247	58% helix, 2% strand	H6UMW9

Pockets

8 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	594	0.70	0.78	53	empty
2	581	0.67	0.77	78	empty
3	212	0.55	0.78	42	empty
4	127	0.55	0.82	20	empty
5	67	0.55	0.87	19	empty

Interfaces

3 interfaces between chains.

B–C · 2072 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1729 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1534 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5Y6J · Structure of Tomato spotted wilt virus nucleocapsid protein with alternative… · 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 H6UMW9
Elsewhere: RCSB PDB 5Y6J · PDBe 5Y6J · UniProt H6UMW9

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