Research workbench
Cryo-EM structure of dktx-bound minimal TRPV1 in partial open state
Analyse Cryo-EM structure of dktx-bound minimal TRPV1 in partial open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2T
- Type
- protein
- Length
- 2,463 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
- XJ7, 65I, NA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transient receptor potential cation channel subfamily V member 1 | protein | 577 | 57% helix, 5% strand | O35433 |
| F, E | Tau-theraphotoxin-HS1A | protein | 75 | 0% helix, 21% strand | P0CH43 |
| B | Transient receptor potential cation channel subfamily V member 1 | protein | 576 | 56% helix, 4% strand | O35433 |
| C | Transient receptor potential cation channel subfamily V member 1 | protein | 576 | 57% helix, 4% strand | O35433 |
| D | Transient receptor potential cation channel subfamily V member 1 | protein | 584 | 57% helix, 4% strand | O35433 |
Ligands and binding sites
- XJ7 · (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2r,3s,4s,5r, 6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate · ligand · 4 copies · chains A, D, B, C
- 65I · (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate · ligand · 4 copies · chains F, B, C, A, E, 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 | 596 | 0.82 | 0.87 | 49 | empty |
| 2 | 952 | 0.80 | 0.82 | 73 | XJ7 |
| 3 | 1145 | 0.80 | 0.81 | 81 | XJ7 |
| 4 | 1108 | 0.80 | 0.81 | 88 | XJ7 |
| 5 | 1195 | 0.79 | 0.81 | 88 | XJ7 |
Interfaces
11 interfaces between chains.
- C–D · 2357 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 2332 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 2319 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 2319 Ų buried · 8 hydrogen bonds · protein-protein
- F–B · 732 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 7L2T · cryo-EM structure of DkTx-bound minimal TRPV1 in partial open state · the same entry in another collection · chain D against D, 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
- P0CH43 · AlphaFold monomer V2.0 prediction for tau-theraphotoxin-HS1A (P0CH43) · a predicted model of the same protein · chain E against A, TM-score 0.79
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 7L2T · PDBe 7L2T · UniProt O35433 · UniProt P0CH43
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