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The crystal structure of penaeus vannamei nodavirus P-domain (P212121)

Analyse The crystal structure of penaeus vannamei nodavirus P-domain (P212121) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YL0
Type: protein
Length: 446 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: A5H7Q8
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	110	0% helix, 51% strand	A5H7Q8
B, C, D	Capsid protein	protein	112	0% helix, 52% strand	A5H7Q8

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.59	0.87	19	empty
2	392	0.55	0.74	43	empty
3	51	0.54	0.89	16	empty

Interfaces

3 interfaces between chains.

C–D · 1288 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1190 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 42 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YL0 · The crystal structure of Penaeus vannamei nodavirus P-domain (P212121) · 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 A5H7Q8
Elsewhere: RCSB PDB 5YL0 · PDBe 5YL0 · UniProt A5H7Q8

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