MolNFT v1 · #144737 · protein
Human GRK2 in complex with gbetagamma subunits and CCG257142
6C2Y · Beta-adrenergic receptor kinase 1: “Human GRK2 in complex with gbetagamma subunits and CCG257142”. X-ray diffraction, 1 ligand (EJS), 10 pockets (best druggability 0.79). MolNFT v1 #144737 on GenesisL1: 3D structure, binding sites…
- PDB
- 6C2Y
- Type
- protein
- Length
- 1,010 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
- EJS
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) | protein | 617 | 45% helix, 16% strand | P25098 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 49% strand | P62871 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 61% helix, 0% strand | P63212 |
Ligands and binding sites
- EJS · (4R,5R,6S)-4-[4-fluoro-3-({[3-(methoxymethyl)-1,2,4-oxadiazol-5-yl]methyl}carbamoyl)phenyl]-N-(2H-indazol-5-yl)-6-methyl-2-oxohexahydropyrimidine-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.79 | 0.85 | 61 | empty |
| 2 | 309 | 0.65 | 0.81 | 37 | EJS |
| 3 | 349 | 0.55 | 0.74 | 37 | empty |
| 4 | 179 | 0.49 | 0.77 | 27 | empty |
| 5 | 203 | 0.47 | 0.75 | 32 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2307 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1142 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6C2Y · Human GRK2 in complex with Gbetagamma subunits and CCG257142 · 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 0.99
- 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 0.68
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 6C2Y · PDBe 6C2Y · UniProt P25098 · UniProt P62871 · UniProt P63212
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