Research workbench
Reconstruction of TRPV1 ion channel in complex with capsaicin by single particle cryo-microscopy
Analyse Reconstruction of TRPV1 ion channel in complex with capsaicin by single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J5R
- Type
- protein
- Length
- 2,368 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
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Transient receptor potential cation channel subfamily V member 1 | protein | 592 | 60% helix, 2% strand | O35433 |
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 | 1108 | 0.87 | 0.88 | 122 | empty |
| 2 | 1086 | 0.81 | 0.82 | 105 | empty |
| 3 | 1025 | 0.79 | 0.80 | 92 | empty |
| 4 | 751 | 0.77 | 0.81 | 63 | empty |
| 5 | 700 | 0.77 | 0.82 | 57 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2194 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 2094 Ų buried · 3 hydrogen bonds · protein-protein
- B–A · 2093 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 2078 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3J5R · Reconstruction of TRPV1 ion channel in complex with capsaicin by single particle… · the same entry in another collection · chain B against B, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 3J5R · PDBe 3J5R · UniProt O35433
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