MolNFT v1 · #59668 · protein
Crystal structure of G protein coupled receptor kinase 1 bound to ATP and magnesium chloride at 2.7A
3C4W · Rhodopsin kinase: “Crystal structure of G protein coupled receptor kinase 1 bound to ATP and magnesium chloride at 2.7A”. X-ray diffraction, 3 ligands (ATP, MG, CL), 11 pockets (best druggability 0.72). MolNFT v1 #59668 on…
- PDB
- 3C4W
- Type
- protein
- Length
- 1,013 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin kinase
- EC
- 2.7.11.14
- UniProt
- P28327
- Ligands
- ATP, MG, CL
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin kinase (EC 2.7.11.14) | protein | 494 | 48% helix, 11% strand | P28327 |
| B | Rhodopsin kinase (EC 2.7.11.14) | protein | 519 | 47% helix, 11% strand | P28327 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.72 | 0.76 | 72 | empty |
| 2 | 457 | 0.70 | 0.81 | 52 | ATP, MG |
| 3 | 351 | 0.63 | 0.79 | 38 | ATP, MG |
| 4 | 219 | 0.59 | 0.80 | 27 | CL |
| 5 | 217 | 0.57 | 0.79 | 31 | CL |
Interfaces
1 interface between chains.
- A–B · 1082 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3C4W · Crystal Structure of G protein coupled receptor kinase 1 bound to ATP and magnesium… · the same entry in another collection · chain A against A, TM-score 1.00
- P28327 · AlphaFold monomer V2.0 prediction for rhodopsin kinase GRK1 (P28327) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P28327
- Elsewhere: RCSB PDB 3C4W · PDBe 3C4W · UniProt P28327
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