MolNFT v1 · #150881 · protein
GI.1 human norovirus protruding domain in complex with nano-62 and 2- fucosyllactose (2FL)
6H70 · Capsid protein VP1: “GI.1 human norovirus protruding domain in complex with nano-62 and 2- fucosyllactose (2FL)”. X-ray diffraction, 4 ligands (GLC, GAL, FUC), 4 pockets (best druggability 0.84). MolNFT v1 #150881 on GenesisL1: 3D…
- PDB
- 6H70
- Type
- protein
- Length
- 827 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Nanobody (vhh) nano-62
- UniProt
- Q83884
- Ligands
- GLC, GAL, FUC, NA
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 290 | 8% helix, 31% strand | Q83884 |
| B | Capsid protein VP1 | protein | 285 | 8% helix, 32% strand | Q83884 |
| C, D | Nanobody (vhh) nano-62 | protein | 126 | 5% helix, 50% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.84 | 0.85 | 121 | EDO |
| 2 | 94 | 0.58 | 0.87 | 24 | empty |
| 3 | 116 | 0.56 | 0.84 | 22 | empty |
| 4 | 58 | 0.27 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1637 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 614 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 593 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 338 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6H70 · GI.1 human norovirus protruding domain in complex with Nano-62 and 2-fucosyllactose (2FL) · 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 Q83884
- Elsewhere: RCSB PDB 6H70 · PDBe 6H70 · UniProt Q83884
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