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Protruding domain of GII.4 human norovirus CHDC2094

Analyse Protruding domain of GII.4 human norovirus CHDC2094 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IYN
Type: protein
Length: 609 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: D0QJ68
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	303	7% helix, 34% strand	D0QJ68
B	VP1	protein	306	5% helix, 36% strand	D0QJ68

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 9 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.69	0.97	22	empty
2	171	0.65	0.86	36	empty
3	239	0.61	0.81	30	empty
4	219	0.59	0.80	31	empty
5	190	0.57	0.80	29	empty

Interfaces

1 interface between chains.

A–B · 1881 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5IYN · Protruding domain of GII.4 human norovirus CHDC2094 · 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 D0QJ68
Elsewhere: RCSB PDB 5IYN · PDBe 5IYN · UniProt D0QJ68

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