Research workbench
Cryo-EM structure of dktx-bound minimal TRPV1 in open state
Analyse Cryo-EM structure of dktx-bound minimal TRPV1 in open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2U
- Type
- protein
- Length
- 2,286 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, XKP, NA
- Pockets
- 20 · best druggability 0.83
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 | 533 | 57% helix, 5% strand | O35433 |
| F, E | Tau-theraphotoxin-HS1A | protein | 75 | 0% helix, 19% strand | P0CH43 |
| B | Transient receptor potential cation channel subfamily V member 1 | protein | 533 | 57% helix, 4% strand | O35433 |
| C | Transient receptor potential cation channel subfamily V member 1 | protein | 538 | 56% helix, 4% strand | O35433 |
| D | Transient receptor potential cation channel subfamily V member 1 | protein | 532 | 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
- XKP · (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate · ligand · 4 copies · chains A, E, D, F, B, C
- NA · Sodium ion · metal · 2 copies · 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 | 1151 | 0.83 | 0.83 | 85 | XJ7 |
| 2 | 1028 | 0.82 | 0.82 | 78 | XJ7 |
| 3 | 1084 | 0.82 | 0.82 | 84 | XJ7 |
| 4 | 835 | 0.81 | 0.83 | 58 | NA |
| 5 | 1172 | 0.81 | 0.82 | 83 | XJ7 |
Interfaces
10 interfaces between chains.
- B–C · 2282 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 2227 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 2222 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 2191 Ų buried · 7 hydrogen bonds · protein-protein
- F–B · 729 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7L2U · cryo-EM structure of DkTx-bound minimal TRPV1 in open state · 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 A against A, TM-score 0.94
- P0CH43 · AlphaFold monomer V2.0 prediction for tau-theraphotoxin-HS1A (P0CH43) · a predicted model of the same protein · chain E against A, TM-score 0.80
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 7L2U · PDBe 7L2U · UniProt O35433 · UniProt P0CH43
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