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Crystal structure of P domain from norovirus GI.9 capsid protein.

Analyse Crystal structure of P domain from norovirus GI.9 capsid protein. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VP0
Type: protein
Length: 620 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: F2XMU3
Ligands: MG
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	VP1	protein	310	8% helix, 33% strand	F2XMU3

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

6 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	345	0.81	0.91	48	empty
2	139	0.77	0.95	36	empty
3	125	0.43	0.76	28	MG
4	161	0.42	0.74	28	empty
5	123	0.40	0.75	28	MG

Interfaces

1 interface between chains.

A–B · 1653 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7VP0 · Crystal structure of P domain from norovirus GI.9 capsid 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 F2XMU3
Elsewhere: RCSB PDB 7VP0 · PDBe 7VP0 · UniProt F2XMU3

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