Research workbench
GII.10 vietnam 026 protruding domain in complex with nanobody nano-14
Analyse GII.10 vietnam 026 protruding domain in complex with nanobody nano-14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMM
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody (vhh) nano-14
- UniProt
- Q5F4T5
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 314 | 7% helix, 35% strand | Q5F4T5 |
| B | Capsid protein | protein | 304 | 8% helix, 37% strand | Q5F4T5 |
| C | Nanobody (vhh) nano-14 | protein | 93 | 0% helix, 43% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, 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 | 1012 | 0.80 | 0.81 | 127 | EDO |
| 2 | 137 | 0.68 | 0.89 | 25 | EDO |
| 3 | 56 | 0.54 | 0.89 | 19 | empty |
| 4 | 183 | 0.52 | 0.78 | 29 | empty |
| 5 | 98 | 0.38 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1873 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 693 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5OMM · GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-14 · 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 5OMM · PDBe 5OMM · UniProt Q5F4T5
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