Research workbench
GI.1 human norovirus protruding domain in complex with nano-94
Analyse GI.1 human norovirus protruding domain in complex with nano-94 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H71
- Type
- protein
- Length
- 812 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
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 285 | 9% helix, 33% strand | Q83884 |
| B | Capsid protein VP1 | protein | 285 | 9% helix, 33% strand | Q83884 |
| C, D | Nanobody (vhh) nano-94 | protein | 121 | 5% helix, 58% strand | — |
Ligands and binding sites
- 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
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 | 546 | 0.78 | 0.84 | 73 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1586 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 960 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 902 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6H71 · GI.1 human norovirus protruding domain in complex with Nano-94 · 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 6H71 · PDBe 6H71 · UniProt Q83884
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