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GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding site

Analyse GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JYO
Type: protein
Length: 1,234 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Norovirus P domain protein
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Norovirus P domain protein	protein	309	7% helix, 36% strand	—
D	Norovirus P domain protein	protein	307	7% helix, 34% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	247	0.76	0.90	34	empty
2	412	0.75	0.85	58	empty
3	241	0.74	0.88	34	empty
4	81	0.72	0.96	27	empty
5	465	0.69	0.80	54	empty

Interfaces

4 interfaces between chains.

B–D · 2258 Å² buried · 39 hydrogen bonds · protein-protein
A–C · 2154 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 223 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 37 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6JYO · GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an… · 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
Elsewhere: RCSB PDB 6JYO · PDBe 6JYO

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