Research workbench
Complex of PKA with the bisubstrate protein kinase inhibitor arc-1411
Analyse Complex of PKA with the bisubstrate protein kinase inhibitor arc-1411 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZJ
- Type
- protein
- Length
- 662 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; 47P-AZ1-dar-dar…
- EC
- 2.7.11.11
- UniProt
- P17612
- Ligands
- 6J9, ZEU, PO4, NH2
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 330 | 40% helix, 16% strand | P17612 |
| B | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 327 | 39% helix, 16% strand | P17612 |
| G | 47P-AZ1-dar-dar | protein | 2 | 0% helix, 0% strand | — |
| F | 47P-AZ1-dar-dar-dar | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 6J9 · 4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine · ligand · 4 copies · chains A, B
- ZEU · 9-hydroxynonanoic acid · ligand · 2 copies · chains A, G, B, F
- PO4 · Phosphate ion · ion · 26 copies · chains A, G, B, F
- NH2 · Amino group · ion · 2 copies · chains G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.77 | 0.85 | 41 | 6J9, ZEU, PO4 |
| 2 | 371 | 0.72 | 0.84 | 39 | 6J9, ZEU, PO4 |
| 3 | 442 | 0.68 | 0.80 | 41 | PO4 |
| 4 | 280 | 0.54 | 0.75 | 38 | empty |
| 5 | 82 | 0.45 | 0.80 | 13 | 6J9 |
Interfaces
3 interfaces between chains.
- A–B · 716 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 276 Ų buried · 1 hydrogen bond · protein-protein
- A–G · 239 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 d-amino, 4 modified, 2 covalent (D-amino acid, phosphorylation, covalent ligand).
Compared structures
- 5IZJ · Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411 · the same entry in another collection · chain B against B, 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 0.97
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 5IZJ · PDBe 5IZJ · UniProt P17612
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