Research workbench
Bovine GRK2 in complex with gbetagamma subunits and a selective kinase inhibitor (CMPD103A)
Analyse Bovine GRK2 in complex with gbetagamma subunits and a selective kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PVW
- Type
- protein
- Length
- 1,012 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
- P21146, P62871, P63212
- Ligands
- QRX
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) | protein | 613 | 45% helix, 15% strand | P21146 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 47% strand | P62871 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 61 | 52% helix, 0% strand | P63212 |
Ligands and binding sites
- QRX · N-(2,6-difluorobenzyl)-3-({[4-propyl-5-(pyrimidin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.78 | 0.84 | 60 | empty |
| 2 | 315 | 0.63 | 0.79 | 35 | QRX |
| 3 | 344 | 0.56 | 0.75 | 32 | empty |
| 4 | 244 | 0.53 | 0.76 | 31 | empty |
| 5 | 102 | 0.51 | 0.82 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2172 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1124 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3PVW · Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor… · 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
- P21146 · AlphaFold monomer V2.0 prediction for beta-adrenergic receptor kinase 1 (P21146) · 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 0.62
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 P21146
- Every structure of UniProt P62871
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 3PVW · PDBe 3PVW · UniProt P21146 · UniProt P62871 · UniProt P63212
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