Research workbench
Crystal structure of the camp-dependent protein kinase a cocrystallized with ATP and pki (5-24)
Analyse Crystal structure of the camp-dependent protein kinase a cocrystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y8C
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P25321, P63248
- Ligands
- ATP, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 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 | 339 | 37% helix, 16% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 18 | 33% helix, 0% strand | P63248 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
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 | 367 | 0.79 | 0.89 | 39 | MG, ATP |
| 2 | 95 | 0.49 | 0.81 | 14 | MPD |
| 3 | 72 | 0.38 | 0.79 | 20 | empty |
| 4 | 51 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6Y8C · Crystal structure of the cAMP-dependent protein kinase A cocrystallized with ATP and PKI… · the same entry in another collection · chain A against A, TM-score 1.00
- P63248 · 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 0.44
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 P25321
- Every structure of UniProt P63248
- Elsewhere: RCSB PDB 6Y8C · PDBe 6Y8C · UniProt P25321 · UniProt P63248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.