Research workbench
2.2 ångström refined crystal structure of the catalytic subunit of camp-dependent protein kinase complexed with mnatp and a peptide inhibitor
Analyse 2.2 ångström refined crystal structure of the catalytic subunit of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ATP
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase; Peptide inhibitor PKI(5-24)
- EC
- 2.7.1.37
- UniProt
- P05132, P63248
- Ligands
- ATP, MN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Camp-dependent protein kinase (EC 2.7.1.37) | protein | 336 | 38% helix, 15% strand | P05132 |
| I | Peptide inhibitor PKI(5-24) | protein | 20 | 30% helix, 0% strand | P63248 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains E, I
- MN · Manganese (II) ion · metal · 2 copies · chains E
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 | 178 | 0.81 | 0.96 | 34 | MN, ATP |
| 2 | 65 | 0.43 | 0.80 | 12 | empty |
| 3 | 98 | 0.42 | 0.78 | 14 | empty |
| 4 | 58 | 0.33 | 0.77 | 13 | empty |
| 5 | 66 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- E–I · 1114 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1ATP · 2.2 angstrom refined crystal structure of the catalytic subunit of cAMP-dependent protein… · the same entry in another collection · chain E against E, TM-score 1.00
- P05132 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain E against A, TM-score 0.99
- P63248 · 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 0.35
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 P05132
- Every structure of UniProt P63248
- Elsewhere: RCSB PDB 1ATP · PDBe 1ATP · UniProt P05132 · UniProt P63248
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