Research workbench
Crystal structure of serotonin 2A receptor in complex with LSD
Analyse Crystal structure of serotonin 2A receptor in complex with LSD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WC6
- Type
- protein
- Length
- 355 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens
- Molecule
- 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
- UniProt
- P28223
- Ligands
- CLR, 7LD, MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 | protein | 355 | 83% helix, 1% strand | P28223 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- 7LD · (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.81 | 0.87 | 53 | 7LD, PEG |
| 2 | 143 | 0.47 | 0.78 | 24 | PEG |
| 3 | 66 | 0.45 | 0.82 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7WC6 · Crystal structure of serotonin 2A receptor in complex with lsd · the same entry in another collection · chain A against A, TM-score 1.00
- P28223 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2A (P28223) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P28223
- Elsewhere: RCSB PDB 7WC6 · PDBe 7WC6 · UniProt P28223
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