MolNFT v1 · #154048 · protein
GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding site
6JYN · Human norovirus P domain protein: “GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding…”. X-ray diffraction, 2 ligands (NAG, GAL), 12 pockets (best druggability 0.85). MolNFT…
- PDB
- 6JYN
- Type
- protein
- Length
- 1,236 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human norovirus P domain protein
- Ligands
- NAG, GAL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Human norovirus P domain protein | protein | 309 | 7% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.85 | 0.90 | 80 | empty |
| 2 | 1165 | 0.84 | 0.85 | 139 | empty |
| 3 | 337 | 0.72 | 0.85 | 44 | empty |
| 4 | 335 | 0.67 | 0.81 | 42 | empty |
| 5 | 135 | 0.49 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2222 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2125 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 529 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 248 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JYN · 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 6JYN · PDBe 6JYN
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