Research workbench
Structure of PKA-pkb chimera complexed with a-443654
Analyse Structure of PKA-pkb chimera complexed with a-443654 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JDV
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase; Camp-dependent protein kinase inhibitor alpha
- EC
- 2.7.11.11
- UniProt
- P00517, P61925
- Ligands
- L20
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase (EC 2.7.11.11) | protein | 336 | 37% helix, 16% strand | P00517 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 35% helix, 0% strand | P61925 |
Ligands and binding sites
- L20 · (2S)-1-(1H-indol-3-yl)-3-{[5-(3-methyl-1H-indazol-5-yl)pyridin-3-yl]oxy}propan-2-amine · ligand · chains A, I
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 | 363 | 0.80 | 0.90 | 51 | L20 |
| 2 | 79 | 0.34 | 0.76 | 15 | empty |
| 3 | 52 | 0.33 | 0.77 | 12 | empty |
| 4 | 75 | 0.32 | 0.74 | 15 | empty |
| 5 | 83 | 0.30 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–I · 1009 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2JDV · Structure of PKA-PKB chimera complexed with A-443654 · the same entry in another collection · chain A against A, TM-score 1.00
- P61925 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain I against A, TM-score 0.42
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 P00517
- Every structure of UniProt P61925
- Elsewhere: RCSB PDB 2JDV · PDBe 2JDV · UniProt P00517 · UniProt P61925
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