Research workbench
Human GRK2 in complex with gbetagamma subunits and CCG222886 (14BD)
Analyse Human GRK2 in complex with gbetagamma subunits and CCG222886 (14BD) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UKL
- Type
- protein
- Length
- 1,031 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, P62873, P59768
- Ligands
- SIX, MG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) | protein | 630 | 45% helix, 16% strand | P25098 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 62 | 58% helix, 0% strand | P59768 |
Ligands and binding sites
- SIX · 2-{5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl) oxy]methyl}piperidin-4-yl]-2-fluorophenyl}-N-[2-(1H-pyrazol-4-yl)ethyl]acetamide · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.79 | 0.84 | 63 | empty |
| 2 | 532 | 0.74 | 0.82 | 55 | SIX |
| 3 | 406 | 0.58 | 0.75 | 50 | empty |
| 4 | 176 | 0.49 | 0.77 | 28 | empty |
| 5 | 223 | 0.48 | 0.74 | 29 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2389 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1247 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5UKL · Human GRK2 in complex with Gbetagamma subunits and CCG222886 (14bd) · the same entry in another collection · chain A against A, 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 0.99
- 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
- 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 G against A, TM-score 0.88
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 P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 5UKL · PDBe 5UKL · UniProt P25098 · UniProt P62873 · UniProt P59768
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