Research workbench
Structure of PKA-pkb chimera complexed with (1-(9H-purin-6- YL)PIPERIDIN-4-YL)AMINE
Analyse Structure of PKA-pkb chimera complexed with (1-(9H-purin-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VNY
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase, alpha-catalytic subunit; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P00517, P61925
- Ligands
- M02
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) | protein | 337 | 37% helix, 16% strand | P00517 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 5% strand | P61925 |
Ligands and binding sites
- M02 · 1-(9H-purin-6-yl)piperidin-4-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.78 | 0.88 | 43 | M02 |
| 2 | 70 | 0.39 | 0.78 | 12 | empty |
| 3 | 80 | 0.36 | 0.77 | 21 | empty |
| 4 | 85 | 0.31 | 0.73 | 17 | empty |
| 5 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–I · 1031 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 2VNY · Structure of PKA-PKB chimera complexed with (1-(9H-Purin-6-yl) piperidin-4-yl)amine · 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 0.41
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 2VNY · PDBe 2VNY · UniProt P00517 · UniProt P61925
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