Research workbench
Crystal structure of G protein-coupled receptor kinase 6 in complex with AMP
Analyse Crystal structure of G protein-coupled receptor kinase 6 in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NYO
- Type
- protein
- Length
- 1,106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G protein-coupled receptor kinase 6
- EC
- 2.7.11.16
- UniProt
- P43250
- Ligands
- ACE, AMP, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | G protein-coupled receptor kinase 6 (EC 2.7.11.16) | protein | 553 | 47% helix, 10% strand | P43250 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.82 | 0.83 | 112 | SO4, BU3 |
| 2 | 981 | 0.80 | 0.82 | 90 | SO4 |
| 3 | 445 | 0.72 | 0.82 | 45 | AMP |
| 4 | 396 | 0.71 | 0.82 | 39 | AMP, SO4 |
| 5 | 200 | 0.68 | 0.86 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 3051 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3NYO · Crystal Structure of G Protein-Coupled Receptor Kinase 6 in Complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P43250 · AlphaFold monomer V2.0 prediction for G protein-coupled receptor kinase 6 (P43250) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P43250
- Elsewhere: RCSB PDB 3NYO · PDBe 3NYO · UniProt P43250
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