MolNFT v1 · #180534 · protein
Cryo-EM structure of dktx-bound minimal TRPV1 at the pre-open state
7L2R · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of dktx-bound minimal TRPV1 at the pre-open state”. Electron microscopy, 3 ligands (XJ7, 65I, NA), 20 pockets (best druggability 0.82). MolNFT v1 #180534…
- PDB
- 7L2R
- Type
- protein
- Length
- 2,611 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 · 4 distinct chains · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transient receptor potential cation channel subfamily V member 1 | protein | 615 | 56% helix, 4% strand | O35433 |
| F, E | Tau-theraphotoxin-HS1A | protein | 75 | 0% helix, 19% strand | P0CH43 |
| B, D | Transient receptor potential cation channel subfamily V member 1 | protein | 614 | 57% helix, 4% strand | O35433 |
| C | Transient receptor potential cation channel subfamily V member 1 | protein | 618 | 56% 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 A, E, B, D, F, C
- 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 | 248 | 0.82 | 0.94 | 27 | empty |
| 2 | 1022 | 0.82 | 0.83 | 77 | XJ7 |
| 3 | 1019 | 0.81 | 0.82 | 78 | XJ7 |
| 4 | 1128 | 0.80 | 0.81 | 91 | XJ7 |
| 5 | 1176 | 0.78 | 0.79 | 81 | XJ7 |
Interfaces
11 interfaces between chains.
- C–D · 2522 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 2498 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 2487 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 2480 Ų buried · 7 hydrogen bonds · protein-protein
- F–B · 671 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7L2R · Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-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 0.80
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 7L2R · PDBe 7L2R · UniProt O35433 · UniProt P0CH43
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