Research workbench
Crystal structure of the lsd-bound 5-HT2B receptor
Analyse Crystal structure of the lsd-bound 5-HT2B receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVN
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera protein of human 5-hydroxytryptamine receptor 2B and E. COLI soluble cytochrome…
- UniProt
- P41595, P0ABE7
- Ligands
- 7LD, CLR, PO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera protein of human 5-hydroxytryptamine receptor 2B and E. COLI soluble cytochrome B562 | protein | 393 | 77% helix, 0% strand | P41595, P0ABE7 |
Ligands and binding sites
- 7LD · (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.78 | 0.86 | 44 | 7LD |
| 2 | 938 | 0.75 | 0.78 | 70 | OLC, PEG |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5TVN · Crystal structure of the LSD-bound 5-HT2B receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P41595 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2B (P41595) · a predicted model of the same protein · chain A against A, TM-score 0.78
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.28
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 P41595
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 5TVN · PDBe 5TVN · UniProt P41595 · UniProt P0ABE7
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