Research workbench
GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-26 and Nano-85
Analyse GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-26… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O04
- Type
- protein
- Length
- 1,076 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Norwalk virus; Vicugna pacos
- Molecule
- Capsid protein; Nanobody (VHH) Nano-26; Nanobody (VHH) Nano-85
- UniProt
- Q5F4T5
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.3 · 6 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 308 | 8% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 315 | 8% helix, 36% strand | Q5F4T5 |
| E | Nanobody (VHH) Nano-26 | protein | 112 | 8% helix, 54% strand | — |
| D | Nanobody (VHH) Nano-85 | protein | 119 | 3% helix, 57% strand | — |
| F | Nanobody (VHH) Nano-26 | protein | 101 | 9% helix, 47% strand | — |
| C | Nanobody (VHH) Nano-85 | protein | 121 | 2% helix, 57% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.79 | 0.81 | 94 | EDO |
| 2 | 951 | 0.78 | 0.80 | 84 | EDO |
| 3 | 307 | 0.59 | 0.77 | 39 | EDO |
| 4 | 106 | 0.50 | 0.82 | 23 | empty |
| 5 | 105 | 0.45 | 0.79 | 22 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 1924 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 741 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 641 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 586 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5O04 · GII.10 vietnam 026 norovirus protruding domain in complex with nanobody nano-26 and… · 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 Q5F4T5
- Elsewhere: RCSB PDB 5O04 · PDBe 5O04 · UniProt Q5F4T5
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