MolNFT v1 · #191352 · protein
Cryo-EM structure of dobutamine-bound BETA1-adrenergic receptor in complex with heterotrimeric gs-protein
8DCR · Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…: “Cryo-EM structure of dobutamine-bound BETA1-adrenergic receptor in complex with heterotrimeric gs-protein”. Electron microscopy, 1 ligand (Y00), 16 pockets (best…
- PDB
- 8DCR
- Type
- protein
- Length
- 1,000 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; Nanobody 35; Guanine…
- EC
- 3.2.1.17
- UniProt
- P62871, P04896, P63212, P00720
- Ligands
- Y00
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 47% strand | P62871 |
| N | Nanobody 35 | protein | 130 | 7% helix, 44% strand | — |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 200 | 47% helix, 19% strand | P04896 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 53% helix, 0% strand | P63212 |
| R | ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera (EC 3.2.1.17) | protein | 275 | 81% helix, 0% strand | P00720 |
Ligands and binding sites
- Y00 · Dobutamine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.82 | 0.85 | 55 | empty |
| 2 | 1128 | 0.77 | 0.79 | 76 | empty |
| 3 | 465 | 0.72 | 0.82 | 66 | empty |
| 4 | 298 | 0.70 | 0.84 | 39 | Y00 |
| 5 | 167 | 0.68 | 0.88 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2207 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 1511 Ų buried · 29 hydrogen bonds · protein-protein
- A–R · 1137 Ų buried · 5 hydrogen bonds · protein-protein
- N–A · 952 Ų buried · 9 hydrogen bonds · protein-protein
- B–N · 589 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 8DCR · Cryo-EM structure of dobutamine-bound beta1-adrenergic receptor in complex with… · the same entry in another collection · chain R against R, TM-score 1.00
- P62871 · 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
- P04896 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.83
- 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 0.61
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 P62871
- Every structure of UniProt P04896
- Every structure of UniProt P63212
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 8DCR · PDBe 8DCR · UniProt P62871 · UniProt P04896 · UniProt P63212 · UniProt P00720
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