MolNFT v1 · #120873 · protein
Bovine GRK2 in complex with gbetagamma subunits and CCG215022
5HE0 · Beta-adrenergic receptor kinase 1: “Bovine GRK2 in complex with gbetagamma subunits and CCG215022”. X-ray diffraction, 1 ligand (453), 10 pockets (best druggability 0.79). MolNFT v1 #120873 on GenesisL1: 3D structure, binding sites…
- PDB
- 5HE0
- Type
- protein
- Length
- 1,020 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, P62873, P59768
- Ligands
- 453
- Pockets
- 10 · 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 | 621 | 45% helix, 16% strand | P21146 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 48% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 60 | 60% helix, 0% strand | P59768 |
Ligands and binding sites
- 453 · (4S)-4-{4-fluoro-3-[(pyridin-2-ylmethyl)carbamoyl]phenyl}-N-(1H-indazol-5-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxamide · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.79 | 0.85 | 59 | empty |
| 2 | 284 | 0.63 | 0.80 | 32 | 453 |
| 3 | 504 | 0.60 | 0.74 | 50 | empty |
| 4 | 234 | 0.50 | 0.75 | 30 | empty |
| 5 | 177 | 0.48 | 0.76 | 29 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2328 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5HE0 · Bovine GRK2 in complex with Gbetagamma subunits and CCG215022 · 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
- 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 0.99
- 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 P21146
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 5HE0 · PDBe 5HE0 · UniProt P21146 · UniProt P62873 · UniProt P59768
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