Research workbench
Human cAMP-dependent protein kinase in complex with an inhibitor
Analyse Human cAMP-dependent protein kinase in complex with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OVV
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.58
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- cAMP-dependent protein kinase catalytic subunit alpha; cAMP-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P17612, P61925
- Ligands
- 1SB, BUD
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.58 · 2 distinct chains · 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 | 337 | 37% helix, 16% strand | P17612 |
| B | cAMP-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 5% strand | P61925 |
Ligands and binding sites
- 1SB · N'-[(1E)-(4-hydroxyphenyl)methylidene]-2-(3-methoxyphenyl)acetohydrazide · ligand · chains A
- BUD · (2S,3S)-butane-2,3-diol · ligand · 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 | 336 | 0.80 | 0.90 | 40 | 1SB, BUD |
| 2 | 81 | 0.47 | 0.81 | 12 | empty |
| 3 | 78 | 0.37 | 0.77 | 16 | empty |
| 4 | 55 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1018 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3OVV · Human camp-dependent protein kinase in complex with an inhibitor · 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
- P61925 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain B against A, TM-score 0.40
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
- Every structure of UniProt P61925
- Elsewhere: RCSB PDB 3OVV · PDBe 3OVV · UniProt P17612 · UniProt P61925
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