Research workbench
Structure of TRPV1 ion channel in complex with dktx and rtx determined by single particle electron cryo-microscopy
Analyse Structure of TRPV1 ion channel in complex with dktx and rtx determined by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J5Q
- Type
- protein
- Length
- 2,492 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 1; Double-knot toxin
- UniProt
- O35433
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, E, G | Transient receptor potential cation channel subfamily V member 1 | protein | 592 | 62% helix, 2% strand | O35433 |
| A, C, F, H | Double-knot toxin | protein | 31 | 0% helix, 26% strand | — |
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 | 939 | 0.85 | 0.86 | 99 | empty |
| 2 | 1020 | 0.83 | 0.83 | 95 | empty |
| 3 | 1004 | 0.82 | 0.83 | 87 | empty |
| 4 | 988 | 0.82 | 0.83 | 101 | empty |
| 5 | 1053 | 0.82 | 0.82 | 103 | empty |
Interfaces
12 interfaces between chains.
- E–G · 2273 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 2263 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 2258 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 2252 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3J5Q · Structure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle… · the same entry in another collection · chain H against H, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain D against A, TM-score 0.90
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 3J5Q · PDBe 3J5Q · UniProt O35433
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