Research workbench
Complex of PKA with the bisubstrate protein kinase inhibitor arc-1408
Analyse Complex of PKA with the bisubstrate protein kinase inhibitor arc-1408 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZF
- Type
- protein
- Length
- 338 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha
- EC
- 2.7.11.11
- UniProt
- P17612
- Ligands
- DAR, 6J9, AZ1, ACA, SO4, NH2
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% 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 | 338 | 37% helix, 15% strand | P17612 |
Ligands and binding sites
- DAR · D-arginine · ligand · 2 copies · chains A
- 6J9 · 4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine · ligand · chains A
- AZ1 · Azelaic acid · ligand · chains A
- ACA · 6-aminohexanoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- NH2 · Amino group · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.69 | 0.81 | 38 | 6J9, AZ1, DAR |
| 2 | 95 | 0.45 | 0.79 | 16 | SO4 |
| 3 | 91 | 0.38 | 0.77 | 19 | empty |
| 4 | 67 | 0.33 | 0.76 | 22 | empty |
| 5 | 80 | 0.32 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5IZF · Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1408 · 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 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 P17612
- Elsewhere: RCSB PDB 5IZF · PDBe 5IZF · UniProt P17612
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