MolNFT v1 · #46732 · protein
Crystal structure of the heterodimeric complex of human RGS8 and activated gi alpha 3
2ODE · Guanine nucleotide-binding protein G(K) subunit alpha: “Crystal structure of the heterodimeric complex of human RGS8 and activated gi alpha 3”. X-ray diffraction, 3 ligands (ALF, GDP, MG), 7 pockets (best druggability 0.85). MolNFT…
- PDB
- 2ODE
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(K) subunit alpha; Regulator of G-protein signaling 8
- UniProt
- P08754, P57771
- Ligands
- ALF, GDP, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(K) subunit alpha | protein | 316 | 51% helix, 15% strand | P08754 |
| B | Regulator of G-protein signaling 8 | protein | 131 | 71% helix, 0% strand | P57771 |
| C | Guanine nucleotide-binding protein G(K) subunit alpha | protein | 317 | 50% helix, 15% strand | P08754 |
| D | Regulator of G-protein signaling 8 | protein | 116 | 72% helix, 0% strand | P57771 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, C
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.85 | 0.86 | 94 | ALF, MG, GDP |
| 2 | 573 | 0.82 | 0.88 | 79 | ALF, MG, GDP |
| 3 | 398 | 0.77 | 0.86 | 41 | empty |
| 4 | 509 | 0.74 | 0.82 | 67 | empty |
| 5 | 214 | 0.63 | 0.82 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 914 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 827 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 366 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 351 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 164 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ODE · Crystal structure of the heterodimeric complex of human RGS8 and activated Gi alpha 3 · the same entry in another collection · chain D against D, TM-score 1.00
- P57771 · AlphaFold monomer V2.0 prediction for regulator of G-protein signaling 8 (P57771) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P08754 · 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 0.99
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 P08754
- Every structure of UniProt P57771
- Elsewhere: RCSB PDB 2ODE · PDBe 2ODE · UniProt P08754 · UniProt P57771
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