MolNFT v1 · #154052 · protein
GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding site
6JYR · Norovirus P domain protein: “GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding…”. X-ray diffraction, 12 pockets (best druggability 0.76). MolNFT v1 #154052 on GenesisL1: 3D…
- PDB
- 6JYR
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Norovirus P domain protein
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Norovirus P domain protein | protein | 308 | 7% helix, 34% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 252 | 0.76 | 0.89 | 36 | empty |
| 2 | 478 | 0.75 | 0.84 | 81 | empty |
| 3 | 143 | 0.53 | 0.81 | 24 | empty |
| 4 | 290 | 0.50 | 0.74 | 26 | empty |
| 5 | 188 | 0.48 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2216 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JYR · 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 6JYR · PDBe 6JYR
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