MolNFT v1 · #142161 · protein

P domain of GII.13 norovirus capsid

5ZV9 · Major capsid protein VP1: “P domain of GII.13 norovirus capsid”. X-ray diffraction, 10 pockets (best druggability 0.76). MolNFT v1 #142161 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZV9
Type: protein
Length: 619 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein VP1
UniProt: A0A0D6CBA8
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein VP1	protein	308	7% helix, 33% strand	A0A0D6CBA8
B	Major capsid protein VP1	protein	311	6% helix, 34% strand	A0A0D6CBA8

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	259	0.76	0.89	34	empty
2	193	0.72	0.89	43	empty
3	200	0.58	0.81	30	empty
4	84	0.57	0.87	20	empty
5	114	0.46	0.79	22	empty

Interfaces

1 interface between chains.

A–B · 2193 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

5ZV9 · P domain of GII.13 norovirus capsid · 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 A0A0D6CBA8
Elsewhere: RCSB PDB 5ZV9 · PDBe 5ZV9 · UniProt A0A0D6CBA8

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