Research workbench
Structure of squirrel TRPV1 in apo state
Analyse Structure of squirrel TRPV1 in apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQY
- Type
- protein
- Length
- 2,636 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osm-9-like TRP channel 1
- UniProt
- I3LZN5
- Ligands
- POV, YBG, NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Osm-9-like TRP channel 1 | protein | 659 | 51% helix, 4% strand | I3LZN5 |
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
- YBG · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A, B, C, D
- CL · Chloride ion · ion · 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 | 1071 | 0.82 | 0.83 | 98 | empty |
| 2 | 150 | 0.82 | 0.98 | 20 | empty |
| 3 | 751 | 0.81 | 0.85 | 71 | YBG, POV |
| 4 | 942 | 0.81 | 0.82 | 81 | YBG, POV |
| 5 | 1010 | 0.80 | 0.81 | 84 | YBG, POV |
Interfaces
6 interfaces between chains.
- C–D · 3420 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 3419 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 3418 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 3418 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LQY · Structure of squirrel TRPV1 in apo state · 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 I3LZN5
- Elsewhere: RCSB PDB 7LQY · PDBe 7LQY · UniProt I3LZN5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.