Research workbench
Structure of TRPV1 in complex with capsazepine, determined in lipid nanodisc
Analyse Structure of TRPV1 in complex with capsazepine, determined in lipid nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IS0
- Type
- protein
- Length
- 1,576 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 1
- UniProt
- O35433
- Ligands
- 6ET
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D, E | Transient receptor potential cation channel subfamily V member 1 | protein | 394 | 60% helix, 3% strand | O35433 |
Ligands and binding sites
- 6ET · capsazepine · ligand · 4 copies · chains C, B, E, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.84 | 0.96 | 32 | empty |
| 2 | 785 | 0.77 | 0.81 | 82 | empty |
| 3 | 750 | 0.77 | 0.81 | 83 | empty |
| 4 | 652 | 0.76 | 0.81 | 77 | empty |
| 5 | 533 | 0.75 | 0.82 | 61 | empty |
Interfaces
6 interfaces between chains.
- B–E · 2051 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 2047 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 2047 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 2042 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5IS0 · Structure of TRPV1 in complex with capsazepine, determined in lipid nanodisc · the same entry in another collection · chain C against C, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain C against A, TM-score 0.95
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 O35433
- Elsewhere: RCSB PDB 5IS0 · PDBe 5IS0 · UniProt O35433
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