Research workbench
GII.10 vietnam 026 norovirus protruding domain in complex with nanobody nano-42
Analyse GII.10 vietnam 026 norovirus protruding domain in complex with nanobody nano-42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O05
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody (vhh) nano-42; Capsid protein
- UniProt
- Q5F4T5
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Nanobody (vhh) nano-42 | protein | 116 | 3% helix, 56% strand | — |
| D | Nanobody (vhh) nano-42 | protein | 114 | 5% helix, 55% strand | — |
| A | Capsid protein | protein | 308 | 6% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 309 | 7% helix, 35% strand | Q5F4T5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 39 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.80 | 0.81 | 117 | EDO |
| 2 | 143 | 0.55 | 0.82 | 22 | EDO |
| 3 | 88 | 0.45 | 0.81 | 21 | EDO |
| 4 | 119 | 0.45 | 0.78 | 20 | EDO |
| 5 | 112 | 0.44 | 0.77 | 24 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1884 Ų buried · 24 hydrogen bonds · protein-protein
- C–B · 648 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 647 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5O05 · GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-42 · the same entry in another collection · chain C against C, 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 5O05 · PDBe 5O05 · UniProt Q5F4T5
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