Research workbench
Crystal structure of the ankyrin repeat domain of chicken TRPV4 in complex with IP3
Analyse Crystal structure of the ankyrin repeat domain of chicken TRPV4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W9F
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanilloid receptor-related osmotically activated channel protein
- UniProt
- Q9DFS3
- Ligands
- I3P
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vanilloid receptor-related osmotically activated channel protein | protein | 255 | 53% helix, 3% strand | Q9DFS3 |
| C | Vanilloid receptor-related osmotically activated channel protein | protein | 249 | 53% helix, 3% strand | Q9DFS3 |
| D | Vanilloid receptor-related osmotically activated channel protein | protein | 249 | 52% helix, 4% strand | Q9DFS3 |
Ligands and binding sites
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · 4 copies · chains A, B, C, D
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 | 249 | 0.56 | 0.77 | 28 | empty |
| 2 | 259 | 0.54 | 0.76 | 28 | empty |
| 3 | 115 | 0.45 | 0.78 | 15 | empty |
| 4 | 142 | 0.45 | 0.76 | 22 | empty |
| 5 | 82 | 0.41 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 485 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 202 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3W9F · Crystal structure of the ankyrin repeat domain of chicken TRPV4 in complex with IP3 · 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 Q9DFS3
- Elsewhere: RCSB PDB 3W9F · PDBe 3W9F · UniProt Q9DFS3
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