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Crystal structure of G protein coupled receptor kinase 1 bound to ADP and magnesium chloride at 2.6A
Analyse Crystal structure of G protein coupled receptor kinase 1 bound to ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C50
- Type
- protein
- Length
- 995 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
- ADP, MG, CL
- Pockets
- 11 · best druggability 0.74
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 | 499 | 47% helix, 11% strand | P28327 |
| B | Rhodopsin kinase (EC 2.7.11.14) | protein | 496 | 48% helix, 11% strand | P28327 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.74 | 0.82 | 52 | ADP, MG |
| 2 | 401 | 0.68 | 0.80 | 44 | ADP, MG |
| 3 | 154 | 0.58 | 0.82 | 22 | CL |
| 4 | 159 | 0.54 | 0.80 | 21 | CL |
| 5 | 242 | 0.48 | 0.74 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1066 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3C50 · Crystal Structure of G protein coupled receptor kinase 1 bound to ADP 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 3C50 · PDBe 3C50 · UniProt P28327
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