Research workbench
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
- 6JYS
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human norovirus P protein
- Ligands
- THR, A2G, GAL, NAG
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Human norovirus P protein | protein | 308 | 6% helix, 34% strand | — |
Ligands and binding sites
- THR · Threonine · ligand · chains B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, D, C
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.76 | 0.96 | 31 | empty |
| 2 | 250 | 0.75 | 0.89 | 32 | empty |
| 3 | 371 | 0.66 | 0.80 | 43 | empty |
| 4 | 381 | 0.62 | 0.77 | 54 | empty |
| 5 | 102 | 0.56 | 0.85 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2235 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 410 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 134 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JYS · GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an… · the same entry in another collection · chain B against B, 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 6JYS · PDBe 6JYS
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