Research workbench
Open apo-state cryo-EM structure of human TRPV6 in glyco-diosgenin detergent
Analyse Open apo-state cryo-EM structure of human TRPV6 in glyco-diosgenin detergent in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S88
- Type
- protein
- Length
- 2,456 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 6
- UniProt
- Q9H1D0
- Ligands
- POV, PCW, Y01, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 6 | protein | 614 | 57% helix, 5% strand | Q9H1D0 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 32 copies · chains A, B, D, C
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 20 copies · chains A, D, B, C
- Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, B, D, C
- CA · Calcium ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.85 | 0.85 | 80 | empty |
| 2 | 1055 | 0.82 | 0.83 | 92 | Y01, PCW |
| 3 | 1023 | 0.82 | 0.82 | 85 | Y01, PCW |
| 4 | 1147 | 0.81 | 0.82 | 103 | Y01, PCW |
| 5 | 1019 | 0.81 | 0.82 | 82 | Y01, PCW |
Interfaces
6 interfaces between chains.
- B–C · 3471 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3469 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 3461 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3454 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7S88 · Open apo-state cryo-EM structure of human TRPV6 in glyco-diosgenin detergent · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H1D0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9H1D0
- Elsewhere: RCSB PDB 7S88 · PDBe 7S88 · UniProt Q9H1D0
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