Research workbench
Structure of chicken Otop3 in nanodiscs
Analyse Structure of chicken Otop3 in nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NF6
- Type
- protein
- Length
- 822 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.32
- Source
- Gallus gallus
- Molecule
- Otopetrin3
- Ligands
- Y01
- Pockets
- 10 · best druggability 0.72
Structure
electron microscopy · resolution 3.32 · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Otopetrin3 | protein | 411 | 78% helix, 0% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.72 | 0.90 | 26 | empty |
| 2 | 153 | 0.72 | 0.90 | 26 | empty |
| 3 | 750 | 0.70 | 0.76 | 68 | Y01 |
| 4 | 294 | 0.68 | 0.83 | 39 | empty |
| 5 | 260 | 0.68 | 0.84 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1446 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6NF6 · Structure of chicken OTOP3 in nanodiscs · 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
- Elsewhere: RCSB PDB 6NF6 · PDBe 6NF6
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