Research workbench
Camp-dependent protein kinase catalytic subunit (E.C.2.7.1.37) (protein kinase a) complexed with protein kinase inhibitor peptide fragment 5-24 (PKI(5-24) isoelectric variant ca) and MN2+ adenylyl imidodiphosphate (mnamp-pnp) at pH 5.6 and 7C and 4C
Analyse Camp-dependent protein kinase catalytic subunit (E.C.2.7.1.37) (protein kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CDK
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase; Protein kinase inhibitor
- EC
- 2.7.11.11
- UniProt
- P00517, P61925
- Ligands
- ANP, MYR, MN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Camp-dependent protein kinase (EC 2.7.11.11) | protein | 343 | 38% helix, 15% strand | P00517 |
| I, J | Protein kinase inhibitor | protein | 20 | 30% helix, 0% strand | P61925 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, I, B, J
- MYR · Myristic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.83 | 0.97 | 43 | MN, ANP |
| 2 | 171 | 0.81 | 0.96 | 33 | MN, ANP |
| 3 | 254 | 0.57 | 0.78 | 37 | MYR |
| 4 | 119 | 0.56 | 0.83 | 18 | MYR |
| 5 | 114 | 0.41 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–J · 1080 Ų buried · 23 hydrogen bonds · protein-protein
- A–I · 1070 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 156 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1CDK · Camp-dependent protein kinase catalytic subunit (E.C.2.7.1.37) (protein kinase a)… · the same entry in another collection · chain A against A, TM-score 1.00
- P00517 · 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
- 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 0.37
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 1CDK · PDBe 1CDK · UniProt P00517 · UniProt P61925
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