Research workbench
Cryo-EM structure of minimal TRPV1 with rtx bound in C2 state
Analyse Cryo-EM structure of minimal TRPV1 with rtx bound in C2 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZD
- Type
- protein
- Length
- 2,128 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
- 6EU, NA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Transient receptor potential cation channel subfamily V member 1 | protein | 532 | 58% helix, 4% strand | O35433 |
Ligands and binding sites
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
- NA · Sodium ion · metal · 2 copies · chains A, D, 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 | 986 | 0.88 | 0.88 | 83 | NA |
| 2 | 154 | 0.74 | 0.91 | 20 | empty |
| 3 | 336 | 0.70 | 0.83 | 35 | empty |
| 4 | 339 | 0.70 | 0.82 | 35 | empty |
| 5 | 327 | 0.69 | 0.83 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2714 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 2695 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2688 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 2682 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MZD · Cryo-EM structure of minimal TRPV1 with RTX bound in C2 state · the same entry in another collection · chain A against A, 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 0.96
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 7MZD · PDBe 7MZD · UniProt O35433
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