Research workbench
Human GRK2 in complex with gbetagamma subunits and CCG258748
Analyse Human GRK2 in complex with gbetagamma subunits and CCG258748 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WG3
- Type
- protein
- Length
- 1,014 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-adrenergic receptor kinase 1; Guanine nucleotide-binding protein G(I)/G(S)/G(T)…
- EC
- 2.7.11.15
- UniProt
- P25098, P62871, P63212
- Ligands
- AFM, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) | protein | 618 | 44% helix, 16% strand | P25098 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 48% strand | P62871 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 56% helix, 0% strand | P63212 |
Ligands and binding sites
- AFM · 2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl) oxy]methyl}piperidin-4-yl]-N-[(1H-pyrazol-3-yl) methyl]benzamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.79 | 0.85 | 60 | empty |
| 2 | 383 | 0.73 | 0.84 | 40 | AFM |
| 3 | 214 | 0.52 | 0.77 | 30 | empty |
| 4 | 179 | 0.45 | 0.75 | 24 | empty |
| 5 | 113 | 0.45 | 0.79 | 28 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2350 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1152 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5WG3 · Human GRK2 in complex with Gbetagamma subunits and CCG258748 · the same entry in another collection · chain A against A, 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
- P25098 · AlphaFold monomer V2.0 prediction for beta-adrenergic receptor kinase 1 (P25098) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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 0.67
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 P25098
- Every structure of UniProt P62871
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 5WG3 · PDBe 5WG3 · UniProt P25098 · UniProt P62871 · UniProt P63212
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