Research workbench
Cryo-EM structure of TRPV5 T709D with PI(4,5)P2 in nanodiscs
Analyse Cryo-EM structure of TRPV5 T709D with PI(4,5)P2 in nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T6Q
- Type
- protein
- Length
- 2,424 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 5
- UniProt
- Q9XSM3
- Ligands
- PIO
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 55% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 5 | protein | 606 | 55% helix, 4% strand | Q9XSM3 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 4 copies · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.84 | 0.85 | 74 | empty |
| 2 | 119 | 0.78 | 0.96 | 26 | empty |
| 3 | 112 | 0.77 | 0.97 | 25 | empty |
| 4 | 112 | 0.77 | 0.97 | 26 | empty |
| 5 | 111 | 0.76 | 0.95 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3408 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 3400 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 3369 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 3362 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7T6Q · Cryo-EM structure of TRPV5 T709D with PI(4,5)P2 in nanodiscs · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XSM3 · 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 Q9XSM3
- Elsewhere: RCSB PDB 7T6Q · PDBe 7T6Q · UniProt Q9XSM3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.