Research workbench
GI.1 human norovirus protruding domain in complex with nano-62
Analyse GI.1 human norovirus protruding domain in complex with nano-62 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H6Z
- Type
- protein
- Length
- 824 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
- NA
- Pockets
- 5 · 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 | 287 | 8% helix, 32% strand | Q83884 |
| B | Capsid protein VP1 | protein | 285 | 7% helix, 32% strand | Q83884 |
| C, D | Nanobody (vhh) nano-62 | protein | 126 | 7% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.84 | 0.84 | 120 | EDO |
| 2 | 89 | 0.59 | 0.87 | 21 | empty |
| 3 | 120 | 0.57 | 0.84 | 22 | empty |
| 4 | 53 | 0.30 | 0.75 | 21 | empty |
| 5 | 63 | 0.29 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1627 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 629 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 613 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 324 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6H6Z · GI.1 human norovirus protruding domain in complex with Nano-62 · 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 6H6Z · PDBe 6H6Z · UniProt Q83884
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