MolNFT v1 · #120874 · protein
Human GRK2 in complex with gbetagamma subunits and CCG224062
5HE1 · Beta-adrenergic receptor kinase 1: “Human GRK2 in complex with gbetagamma subunits and CCG224062”. X-ray diffraction, 2 ligands (ZS2, MG), 10 pockets (best druggability 0.80). MolNFT v1 #120874 on GenesisL1: 3D structure, binding…
- PDB
- 5HE1
- Type
- protein
- Length
- 1,019 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
- ZS2, MG
- Pockets
- 10 · best druggability 0.80
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 | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 62 | 50% helix, 0% strand | P59768 |
Ligands and binding sites
- ZS2 · (4~{S})-4-[4-fluoranyl-3-(isoquinolin-1-ylmethylcarbamoyl)phenyl]-~{N}-(1~{H}-indazol-5-yl)-6-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-pyrimidine-5-carboxamide · 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
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 | 576 | 0.80 | 0.85 | 57 | empty |
| 2 | 349 | 0.64 | 0.79 | 36 | ZS2 |
| 3 | 451 | 0.58 | 0.74 | 54 | empty |
| 4 | 218 | 0.52 | 0.77 | 29 | empty |
| 5 | 171 | 0.47 | 0.76 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2410 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1101 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5HE1 · Human GRK2 in complex with Gbetagamma subunits and CCG224062 · the same entry in another collection · chain B against B, 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 0.87
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 5HE1 · PDBe 5HE1 · UniProt P25098 · UniProt P62873 · UniProt P59768
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