Research workbench
Cryo-EM structure of DKTX/RTX-bound full-length TRPV1
Analyse Cryo-EM structure of DKTX/RTX-bound full-length TRPV1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2M
- Type
- protein
- Length
- 1,934 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
- 6EU, NA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, B | Transient receptor potential cation channel subfamily V member 1 | protein | 446 | 59% helix, 4% strand | O35433 |
| E, F | Tau-theraphotoxin-HS1A | protein | 75 | 0% helix, 21% strand | P0CH43 |
Ligands and binding sites
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
- NA · Sodium ion · metal · 3 copies · chains A, C, D, B
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 | 931 | 0.83 | 0.84 | 77 | NA |
| 2 | 1046 | 0.81 | 0.82 | 86 | empty |
| 3 | 1027 | 0.80 | 0.81 | 81 | empty |
| 4 | 1180 | 0.79 | 0.81 | 79 | empty |
| 5 | 993 | 0.79 | 0.80 | 66 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2009 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 1933 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 1929 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1924 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 622 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7L2M · Cryo-EM structure of DkTx/RTX-bound full-length TRPV1 · 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 0.74
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 7L2M · PDBe 7L2M · UniProt O35433 · UniProt P0CH43
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