Research workbench
Cryo-EM structure of unliganded full-length TRPV1 at neutral pH
Analyse Cryo-EM structure of unliganded full-length TRPV1 at neutral pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2H
- Type
- protein
- Length
- 2,123 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
- XJ7, XJD, NA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C | Transient receptor potential cation channel subfamily V member 1 | protein | 531 | 58% helix, 5% strand | O35433 |
| B | Transient receptor potential cation channel subfamily V member 1 | protein | 530 | 58% helix, 6% strand | O35433 |
Ligands and binding sites
- XJ7 · (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2r,3s,4s,5r, 6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate · ligand · 4 copies · chains A, D, C, B
- XJD · (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl tridecanoate · ligand · 4 copies · chains A, D, C, B
- NA · Sodium ion · metal · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.83 | 0.97 | 27 | empty |
| 2 | 983 | 0.81 | 0.82 | 93 | XJ7 |
| 3 | 867 | 0.80 | 0.83 | 79 | XJ7 |
| 4 | 951 | 0.80 | 0.81 | 90 | XJ7 |
| 5 | 659 | 0.75 | 0.81 | 59 | XJ7 |
Interfaces
6 interfaces between chains.
- A–D · 2642 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2626 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 2610 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 2584 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7L2H · Cryo-EM structure of unliganded full-length TRPV1 at neutral pH · 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 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 7L2H · PDBe 7L2H · UniProt O35433
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