MolNFT v1 · #179116 · protein
Cryo-EM structure of bromocriptine-bound dopamine receptor 2 in complex with gi protein
7JVR · Soluble cytochrome B562,D(2) dopamine receptor: “Cryo-EM structure of bromocriptine-bound dopamine receptor 2 in complex with gi protein”. Electron microscopy, 1 ligand (08Y), 14 pockets (best druggability 0.82). MolNFT v1 #179116…
- PDB
- 7JVR
- Type
- protein
- Length
- 1,126 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,D(2) dopamine receptor; Guanine nucleotide-binding protein G(I)…
- UniProt
- P14416, P63096, P62873, P59768
- Ligands
- 08Y
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Soluble cytochrome B562,D(2) dopamine receptor | protein | 269 | 86% helix, 0% strand | P14416 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 224 | 50% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 342 | 6% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 53% helix, 0% strand | P59768 |
| E | Antibody fragment SCFV16 | protein | 233 | 0% helix, 45% strand | — |
Ligands and binding sites
- 08Y · bromoergocryptine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.82 | 0.86 | 70 | empty |
| 2 | 573 | 0.78 | 0.84 | 40 | 08Y |
| 3 | 976 | 0.77 | 0.80 | 75 | empty |
| 4 | 249 | 0.53 | 0.76 | 35 | empty |
| 5 | 138 | 0.53 | 0.81 | 32 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2437 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 14 hydrogen bonds · protein-protein
- R–A · 1147 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 616 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 495 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7JVR · Cryo-EM structure of Bromocriptine-bound dopamine receptor 2 in complex with Gi protein · 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 B against A, TM-score 0.98
- 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 C against A, TM-score 0.95
- P14416 · AlphaFold monomer V2.0 prediction for D(2) dopamine receptor (P14416) · a predicted model of the same protein · chain R against A, TM-score 0.91
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P14416
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7JVR · PDBe 7JVR · UniProt P14416 · UniProt P63096 · UniProt P62873 · UniProt P59768
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