Research workbench
Structure of squirrel TRPV1 in complex with capsaicin
Analyse Structure of squirrel TRPV1 in complex with capsaicin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LR0
- Type
- protein
- Length
- 2,584 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, 4DY, NA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 53% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Osm-9-like TRP channel 1 | protein | 646 | 53% helix, 4% strand | I3LZN5 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 28 copies · chains A, B, C, D
- 4DY · (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.88 | 0.89 | 100 | NA |
| 2 | 361 | 0.76 | 0.86 | 38 | POV |
| 3 | 468 | 0.75 | 0.84 | 56 | POV |
| 4 | 358 | 0.74 | 0.85 | 41 | POV |
| 5 | 479 | 0.74 | 0.83 | 53 | POV |
Interfaces
6 interfaces between chains.
- A–D · 3153 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3145 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 3121 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 3110 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LR0 · Structure of squirrel TRPV1 in complex with capsaicin · 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 7LR0 · PDBe 7LR0 · UniProt I3LZN5
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