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Structural basis for norovirus inhibition and fucose mimicry by citrate

Analyse Structural basis for norovirus inhibition and fucose mimicry by citrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RY8
Type: protein
Length: 611 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: Q5F4T5
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	310	8% helix, 38% strand	Q5F4T5
B	Capsid protein	protein	301	6% helix, 36% strand	Q5F4T5

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
FLC · Citrate anion · additive · chains A, B

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

Pockets

3 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	1055	0.79	0.81	117	EDO
2	113	0.56	0.84	21	empty
3	92	0.38	0.76	23	empty

Interfaces

1 interface between chains.

A–B · 1917 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3RY8 · Structural basis for norovirus inhibition and fucose mimicry by citrate · 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 Q5F4T5
Elsewhere: RCSB PDB 3RY8 · PDBe 3RY8 · UniProt Q5F4T5

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