MolNFT v1 · #142591 · protein
Crystal structure of 5-HT2AR in complex with risperidone
6A93 · 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562: “Crystal structure of 5-HT2AR in complex with risperidone”. X-ray diffraction, 4 ligands (8NU, CLR, PLM), 6 pockets (best druggability 0.81). MolNFT v1 #142591 on GenesisL1…
- PDB
- 6A93
- Type
- protein
- Length
- 729 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562
- UniProt
- P28223, P0ABE7
- Ligands
- 8NU, CLR, PLM, ZN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562 | protein | 370 | 83% helix, 1% strand | P28223, P0ABE7 |
| B | 5-hydroxytryptamine receptor 2A,SOLUBLE cytochrome B562 | protein | 359 | 84% helix, 1% strand | P28223, P0ABE7 |
Ligands and binding sites
- 8NU · 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one · ligand · 2 copies · chains A, B
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.81 | 0.86 | 51 | 8NU, 1PE |
| 2 | 555 | 0.80 | 0.86 | 50 | 8NU |
| 3 | 435 | 0.64 | 0.77 | 40 | empty |
| 4 | 218 | 0.54 | 0.78 | 24 | empty |
| 5 | 88 | 0.50 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 242 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 lipid (disulfide, palmitoylation).
Compared structures
- 6A93 · Crystal structure of 5-HT2AR in complex with risperidone · 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 B against A, TM-score 0.86
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.26
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
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6A93 · PDBe 6A93 · UniProt P28223 · UniProt P0ABE7
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