Research workbench
Cryo-EM structure of the full-length TRPV1 with rtx at 4 degrees celsius, in an intermediate-closed state, class II
Analyse Cryo-EM structure of the full-length TRPV1 with rtx at 4 degrees celsius, in an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RQV
- Type
- protein
- Length
- 2,320 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
- 6OU, LBN, 6EU, NA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 53% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, B | Transient receptor potential cation channel subfamily V member 1 | protein | 580 | 53% helix, 4% strand | O35433 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 12 copies · chains A, D, B, C
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, C, D, B
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
- NA · Sodium ion · metal · 2 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 | 679 | 0.84 | 0.88 | 51 | NA |
| 2 | 698 | 0.78 | 0.82 | 62 | LBN |
| 3 | 664 | 0.78 | 0.83 | 59 | LBN |
| 4 | 655 | 0.77 | 0.82 | 57 | LBN |
| 5 | 630 | 0.76 | 0.82 | 57 | LBN |
Interfaces
4 interfaces between chains.
- A–B · 2476 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 2475 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 2474 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 2472 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7RQV · Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in an… · 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 7RQV · PDBe 7RQV · UniProt O35433
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