Research workbench
Cryo-EM structure of the 5HT2C receptor (vsv isoform) bound to lorcaserin
Analyse Cryo-EM structure of the 5HT2C receptor (vsv isoform) bound to lorcaserin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DPI
- Type
- protein
- Length
- 1,093 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 2C; G-alpha subunit Q (GI2-mini-gq chimera); Guanine…
- UniProt
- P28335, P62873, P59768
- Ligands
- T4U, CLR
- Pockets
- 13 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2C | protein | 264 | 81% helix, 1% strand | P28335 |
| B | G-alpha subunit Q (GI2-mini-gq chimera) | protein | 221 | 47% helix, 19% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 48% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 42 | 57% helix, 0% strand | P59768 |
| E | Antibody fragment SCFV16 | protein | 230 | 3% helix, 50% strand | — |
Ligands and binding sites
- T4U · (1R)-8-chloro-1-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine · ligand · chains A
- CLR · Cholesterol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.83 | 0.84 | 65 | empty |
| 2 | 599 | 0.78 | 0.83 | 51 | T4U |
| 3 | 57 | 0.72 | 0.98 | 18 | empty |
| 4 | 466 | 0.61 | 0.75 | 62 | empty |
| 5 | 179 | 0.59 | 0.82 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1817 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1181 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1040 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 540 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 354 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 8DPI · Cryo-EM structure of the 5HT2C receptor (VSV isoform) bound to lorcaserin · the same entry in another collection · chain E against E, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P28335 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2C (P28335) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain D against A, TM-score 0.87
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 P28335
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 8DPI · PDBe 8DPI · UniProt P28335 · UniProt P62873 · UniProt P59768
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