Research workbench
Cryoem structure of go-coupled 5-HT5AR in complex with 5-ct
Analyse Cryoem structure of go-coupled 5-HT5AR in complex with 5-ct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UM5
- Type
- protein
- Length
- 1,104 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
- 8K3
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 5A | protein | 268 | 76% helix, 1% strand | P47898 |
| B | Minigo protein | protein | 214 | 38% helix, 20% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 48% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 61% helix, 0% strand | P59768 |
| E | Single-chain variable fragment SCFV16 | protein | 230 | 3% helix, 50% strand | — |
Ligands and binding sites
- 8K3 · 3-(2-azanylethyl)-1H-indole-5-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.82 | 0.84 | 60 | empty |
| 2 | 591 | 0.78 | 0.84 | 49 | 8K3 |
| 3 | 320 | 0.62 | 0.79 | 48 | empty |
| 4 | 175 | 0.61 | 0.83 | 21 | empty |
| 5 | 235 | 0.58 | 0.79 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2045 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1076 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 727 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 534 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 391 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7UM5 · CryoEM structure of Go-coupled 5-HT5AR in complex with 5-CT · 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 0.95
- 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 0.83
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 7UM5 · PDBe 7UM5 · UniProt P47898 · UniProt P62873 · UniProt P59768
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.