Research workbench
Open apo-state cryo-EM structure of human TRPV6 in CNW11 nanodiscs
Analyse Open apo-state cryo-EM structure of human TRPV6 in CNW11 nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S89
- Type
- protein
- Length
- 2,376 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, Y01, PCW, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 6 | protein | 594 | 58% helix, 6% strand | Q9H1D0 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 28 copies · chains A, D, B, C
- Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, B, D, C
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B, C, D
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.85 | 0.86 | 62 | empty |
| 2 | 1047 | 0.77 | 0.78 | 70 | Y01 |
| 3 | 1064 | 0.77 | 0.78 | 81 | Y01 |
| 4 | 1123 | 0.76 | 0.78 | 84 | Y01 |
| 5 | 1121 | 0.76 | 0.78 | 82 | Y01 |
Interfaces
6 interfaces between chains.
- C–D · 3420 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3404 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 3403 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 3401 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7S89 · Open apo-state cryo-EM structure of human TRPV6 in cNW11 nanodiscs · 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 0.99
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 7S89 · PDBe 7S89 · UniProt Q9H1D0
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