Research workbench
GI.1 human norovirus protruding domain in complex with nano-94 and 2- fucosyllactose (2FL)
Analyse GI.1 human norovirus protruding domain in complex with nano-94 and 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H72
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Nanobody (vhh) nano-94
- UniProt
- Q83884
- Ligands
- GLC, GAL, FUC
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein VP1 | protein | 290 | 9% helix, 32% strand | Q83884 |
| C | Nanobody (vhh) nano-94 | protein | 121 | 5% helix, 59% strand | — |
| D | Nanobody (vhh) nano-94 | protein | 120 | 5% helix, 58% 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
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.77 | 0.84 | 80 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1650 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 907 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6H72 · GI.1 human norovirus protruding domain in complex with Nano-94 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 6H72 · PDBe 6H72 · UniProt Q83884
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.