MolNFT v1 · #186338 · protein
5-HT2AR bound to a novel agonist in complex with a mini-gq protein and an active-state stabilizing single-chain variable fragment (SCFV16) obtained by cryo-electron microscopy (cryoem)
7RAN · 5-hydroxytryptamine receptor 2A: “5-HT2AR bound to a novel agonist in complex with a mini-gq protein and an active-state stabilizing…”. Electron microscopy, 1 ligand (3IQ), 13 pockets (best druggability 0.81). MolNFT v1 #186338 on…
- PDB
- 7RAN
- Type
- protein
- Length
- 1,120 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 2A; G protein subunit Q (GI2-mini-gq chimera); Guanine…
- UniProt
- P28223, P62873, P59768
- Ligands
- 3IQ
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 2A | protein | 269 | 84% helix, 0% strand | P28223 |
| B | G protein subunit Q (GI2-mini-gq chimera) | protein | 232 | 39% helix, 17% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 46% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 51% helix, 0% strand | P59768 |
| E | Single-chain variable fragment 16 (SCFV16) | protein | 228 | 0% helix, 41% strand | — |
Ligands and binding sites
- 3IQ · (3R)-3-methyl-5-(1H-pyrrolo[2,3-b]pyridin-3-yl)-1,2,3, 6-tetrahydropyridin-1-ium · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.81 | 0.82 | 68 | empty |
| 2 | 110 | 0.79 | 0.98 | 20 | empty |
| 3 | 619 | 0.76 | 0.82 | 49 | 3IQ |
| 4 | 944 | 0.73 | 0.77 | 99 | empty |
| 5 | 128 | 0.72 | 0.92 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1933 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1208 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1205 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 532 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 407 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RAN · 5-HT2AR bound to a novel agonist in complex with a mini-Gq protein and an active-state… · 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 0.98
- 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 0.91
- 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 0.76
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 P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7RAN · PDBe 7RAN · UniProt P28223 · UniProt P62873 · UniProt P59768
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