Research workbench
Structure of TRPV1 in complex with dktx and rtx, determined in lipid nanodisc
Analyse Structure of TRPV1 in complex with dktx and rtx, 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
- 5IRX
- Type
- protein
- Length
- 1,726 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 1; Tau-theraphotoxin-HS1A
- UniProt
- O35433, P0CH43
- Ligands
- 6OE, 6O8, 6EU, 6O9
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 1 | protein | 394 | 59% helix, 5% strand | O35433 |
| E, F | Tau-theraphotoxin-HS1A | protein | 75 | 0% helix, 19% strand | P0CH43 |
Ligands and binding sites
- 6OE · (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate · ligand · 8 copies · chains A, C, F, B, D, E
- 6O8 · (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium · ligand · 4 copies · chains A, B, C, D
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, B, D, C
- 6O9 · (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate · ligand · 4 copies · chains D, E, C, B, F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.80 | 0.82 | 69 | empty |
| 2 | 944 | 0.80 | 0.81 | 82 | 6O8 |
| 3 | 824 | 0.79 | 0.82 | 69 | 6O8 |
| 4 | 909 | 0.79 | 0.81 | 73 | 6O8 |
| 5 | 796 | 0.78 | 0.82 | 63 | 6O8 |
Interfaces
10 interfaces between chains.
- A–C · 1814 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1808 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1804 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1799 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 639 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 covalent (disulfide, covalent ligand).
Compared structures
- 5IRX · Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc · the same entry in another collection · chain F against F, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.92
- P0CH43 · AlphaFold monomer V2.0 prediction for tau-theraphotoxin-HS1A (P0CH43) · a predicted model of the same protein · chain F against A, TM-score 0.80
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
- Every structure of UniProt P0CH43
- Elsewhere: RCSB PDB 5IRX · PDBe 5IRX · UniProt O35433 · UniProt P0CH43
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