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Crystal structure of an artificial top component of turnip yellow mosaic virus

Analyse Crystal structure of an artificial top component of turnip yellow mosaic virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W39
Type: protein
Length: 547 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Turnip yellow mosaic virus empty capsid
UniProt: P03608
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Turnip yellow mosaic virus empty capsid	protein	169	9% helix, 43% strand	P03608
B, C	Turnip yellow mosaic virus empty capsid	protein	189	10% helix, 41% strand	P03608

Pockets

5 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	372	0.58	0.76	41	empty
2	100	0.36	0.74	22	empty
3	80	0.36	0.76	18	empty
4	87	0.35	0.75	18	empty
5	63	0.29	0.74	20	empty

Interfaces

3 interfaces between chains.

B–C · 1032 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 822 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 819 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1W39 · Crystal structure of an artificial top component of turnip yellow mosaic 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 P03608
Elsewhere: RCSB PDB 1W39 · PDBe 1W39 · UniProt P03608

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