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Protruding domain of GII.4 human norovirus isolate 08-14

Analyse Protruding domain of GII.4 human norovirus isolate 08-14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KON
Type: protein
Length: 620 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.51
Source: Norovirus GII.4
Molecule: VP1
UniProt: A0A0N9DUX3
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · resolution 1.51 · 1 distinct chain · 5% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	VP1	protein	310	5% helix, 35% strand	A0A0N9DUX3

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.78	0.97	22	EDO
2	53	0.72	0.99	22	empty
3	416	0.68	0.81	48	EDO, MES
4	415	0.68	0.81	55	EDO, MES
5	79	0.34	0.75	16	EDO

Interfaces

1 interface between chains.

A–B · 1937 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5KON · Protruding domain of GII.4 human norovirus isolate 08-14 · 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 A0A0N9DUX3
Elsewhere: RCSB PDB 5KON · PDBe 5KON · UniProt A0A0N9DUX3

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