MolNFT v1 · #122528 · protein
Structure of TRPV1 in complex with dktx and rtx, determined in lipid nanodisc
5IRX · Transient receptor potential cation channel subfamily V…: “Structure of TRPV1 in complex with dktx and rtx, determined in lipid nanodisc”. Electron microscopy, 4 ligands (6OE, 6O8, 6EU), 20 pockets (best druggability 0.80). MolNFT…
- 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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