Research workbench
Cryoem structure of go-coupled 5-HT5AR in complex with methylergometrine
Analyse Cryoem structure of go-coupled 5-HT5AR in complex with methylergometrine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UM7
- Type
- protein
- Length
- 1,089 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 5A; Minigo protein; Guanine nucleotide-binding protein…
- UniProt
- P47898, P62873, P59768
- Ligands
- H8D
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 5A | protein | 256 | 77% helix, 0% strand | P47898 |
| B | Minigo protein | protein | 214 | 39% helix, 20% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 47% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 55% helix, 0% strand | P59768 |
| E | Single-chain variable fragment SCFV16 | protein | 230 | 3% helix, 49% strand | — |
Ligands and binding sites
- H8D · (8beta)-N-[(2S)-1-hydroxybutan-2-yl]-6-methyl-9,10-didehydroergoline-8-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.82 | 0.83 | 62 | empty |
| 2 | 521 | 0.73 | 0.81 | 38 | H8D |
| 3 | 272 | 0.68 | 0.83 | 31 | empty |
| 4 | 315 | 0.60 | 0.78 | 45 | empty |
| 5 | 124 | 0.58 | 0.85 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2035 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1096 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 721 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 533 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 395 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7UM7 · CryoEM structure of Go-coupled 5-HT5AR in complex with Methylergometrine · 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
- P47898 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 5A (P47898) · a predicted model of the same protein · chain A against A, TM-score 0.94
- 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 0.85
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 P47898
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7UM7 · PDBe 7UM7 · UniProt P47898 · UniProt P62873 · UniProt P59768
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