Research workbench
Dog BETA3 adrenergic receptor bound to mirabegron in complex with a minigs heterotrimer
Analyse Dog BETA3 adrenergic receptor bound to mirabegron in complex with a minigs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DH5
- Type
- protein
- Length
- 1,027 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms SHORT,GUANINE…
- UniProt
- P63092, P54311, P63212, O02662
- Ligands
- H6U
- Pockets
- 9 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms SHORT,GUANINE nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 231 | 45% helix, 16% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 9% helix, 38% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 52 | 58% helix, 0% strand | P63212 |
| N | Nanobody NB35 | protein | 128 | 7% helix, 37% strand | — |
| R | Beta-3 adrenergic receptor | protein | 276 | 73% helix, 0% strand | O02662 |
Ligands and binding sites
- H6U · 2-(2-azanyl-1,3-thiazol-4-yl)-N-[4-[2-[[(2R)-2-oxidanyl-2-phenyl-ethyl]amino]ethyl]phenyl]ethanamide · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.84 | 0.85 | 78 | empty |
| 2 | 1025 | 0.76 | 0.79 | 76 | empty |
| 3 | 403 | 0.73 | 0.84 | 60 | H6U |
| 4 | 451 | 0.71 | 0.81 | 58 | empty |
| 5 | 624 | 0.65 | 0.75 | 51 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2159 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 16 hydrogen bonds · protein-protein
- A–R · 1319 Ų buried · 9 hydrogen bonds · protein-protein
- A–N · 748 Ų buried · 4 hydrogen bonds · protein-protein
- B–N · 440 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7DH5 · Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer · the same entry in another collection · chain R against R, TM-score 1.00
- P54311 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- O02662 · AlphaFold monomer V2.0 prediction for beta-3 adrenergic receptor (O02662) · a predicted model of the same protein · chain R against A, TM-score 0.91
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.65
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 P63092
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Every structure of UniProt O02662
- Elsewhere: RCSB PDB 7DH5 · PDBe 7DH5 · UniProt P63092 · UniProt P54311 · UniProt P63212 · UniProt O02662
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