Research workbench
GII.10 vietnam 026 protruding domain in complex with nanobody nano-27
Analyse GII.10 vietnam 026 protruding domain in complex with nanobody nano-27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMN
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody (vhh) nano-27
- UniProt
- Q5F4T5
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Capsid protein | protein | 312 | 6% helix, 35% strand | Q5F4T5 |
| C | Nanobody (vhh) nano-27 | protein | 113 | 3% helix, 51% strand | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.40 | 0.77 | 22 | empty |
| 2 | 86 | 0.35 | 0.74 | 16 | empty |
| 3 | 69 | 0.28 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- B–C · 570 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5OMN · GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27 · the same entry in another collection · chain B against B, 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 5OMN · PDBe 5OMN · UniProt Q5F4T5
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