Research workbench
X-ray structure of camp dependent protein kinase a in complex with high na+ concentration, ADP and phosphorylated peptide PSP20
Analyse X-ray structure of camp dependent protein kinase a in complex with high na+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IB0
- 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; Phosphorylated pseudo-substrate…
- EC
- 2.7.11.11
- UniProt
- P05132
- Ligands
- ADP, NA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 337 | 36% helix, 16% strand | P05132 |
| S | Phosphorylated pseudo-substrate peptide PSP20 | protein | 20 | 30% helix, 10% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, S
- NA · Sodium ion · metal · 2 copies · chains A, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.81 | 0.95 | 41 | NA, ADP |
| 2 | 90 | 0.44 | 0.80 | 19 | empty |
| 3 | 80 | 0.42 | 0.78 | 12 | empty |
| 4 | 66 | 0.29 | 0.74 | 14 | empty |
| 5 | 52 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–S · 1098 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 4IB0 · X-ray Structure of cAMP dependent protein kinase A in complex with high Na+… · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 4IB0 · PDBe 4IB0 · UniProt P05132
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