Research workbench
Cryo-EM structure of dktx-bound minimal TRPV1 at the pre-bound state
Analyse Cryo-EM structure of dktx-bound minimal TRPV1 at the pre-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2S
- Type
- protein
- Length
- 2,506 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
- XJ7, 6IY, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | Transient receptor potential cation channel subfamily V member 1 | protein | 626 | 57% helix, 4% strand | O35433 |
| C | Transient receptor potential cation channel subfamily V member 1 | protein | 628 | 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 D, C, A, B
- 6IY · (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate · ligand · 4 copies · chains D, A, B, C
- NA · Sodium ion · metal · chains D, A, B, C
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 | 343 | 0.85 | 0.95 | 32 | empty |
| 2 | 981 | 0.82 | 0.83 | 82 | XJ7 |
| 3 | 1120 | 0.80 | 0.81 | 80 | XJ7 |
| 4 | 1196 | 0.79 | 0.81 | 89 | XJ7 |
| 5 | 1166 | 0.79 | 0.80 | 90 | XJ7 |
Interfaces
6 interfaces between chains.
- A–B · 2890 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 2841 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 2828 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 2796 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7L2S · cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-bound 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
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 7L2S · PDBe 7L2S · UniProt O35433
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