MolNFT v1 · #186815 · protein
Cryo-EM structure of the full-length TRPV1 with rtx at 48 degrees celsius, in an open state, class alpha
7RQZ · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of the full-length TRPV1 with rtx at 48 degrees celsius, in an open state, class alpha”. Electron microscopy, 3 ligands (LBN, 6OU, 6EU), 20 pockets (best…
- PDB
- 7RQZ
- 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
- LBN, 6OU, 6EU
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Transient receptor potential cation channel subfamily V member 1 | protein | 532 | 58% helix, 3% strand | O35433 |
Ligands and binding sites
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains A, C, B, D
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 8 copies · chains A, C, B, D
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, C, B, 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 | 970 | 0.83 | 0.84 | 75 | empty |
| 2 | 586 | 0.78 | 0.84 | 60 | LBN |
| 3 | 552 | 0.73 | 0.81 | 75 | empty |
| 4 | 535 | 0.72 | 0.80 | 51 | 6EU |
| 5 | 579 | 0.72 | 0.80 | 74 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2238 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 2237 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 2236 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 2236 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RQZ · Cryo-EM structure of the full-length TRPV1 with RTx at 48 degrees Celsius, in an open… · 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 0.93
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 7RQZ · PDBe 7RQZ · UniProt O35433
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