MolNFT v1 · #122981 · protein
Complex of PKA with the bisubstrate protein kinase inhibitor arc-1416
5J5X · Camp-dependent protein kinase catalytic subunit alpha: “Complex of PKA with the bisubstrate protein kinase inhibitor arc-1416”. X-ray diffraction, 4 ligands (6J9, ZEU, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #122981 on…
- PDB
- 5J5X
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; 47P-AZ1-dal-dar-dar-dar-dar
- EC
- 2.7.11.11
- UniProt
- P17612
- Ligands
- 6J9, ZEU, SO4, NH2
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 342 | 37% helix, 15% strand | P17612 |
| B | 47P-AZ1-dal-dar-dar-dar-dar | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- 6J9 · 4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine · ligand · 2 copies · chains A, B
- ZEU · 9-hydroxynonanoic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.75 | 0.86 | 54 | 6J9, ZEU |
| 2 | 137 | 0.46 | 0.77 | 17 | 6J9 |
| 3 | 61 | 0.31 | 0.76 | 17 | empty |
| 4 | 57 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 d-amino, 2 modified, 1 covalent (D-amino acid, phosphorylation, covalent ligand).
Compared structures
- 5J5X · Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1416 · the same entry in another collection · chain A against A, TM-score 1.00
- P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P17612
- Elsewhere: RCSB PDB 5J5X · PDBe 5J5X · UniProt P17612
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