MolNFT v1 · #20402 · protein
Hydrolysis of ATP in the crystal of Y204A mutant of camp-dependent protein kinase
1RDQ · Camp-dependent protein kinase, alpha-catalytic subunit: “Hydrolysis of ATP in the crystal of Y204A mutant of camp-dependent protein kinase”. X-ray diffraction, 4 ligands (ADP, ATP, MG), 4 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 1RDQ
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase, alpha-catalytic subunit; Camp-dependent protein kinase…
- EC
- 2.7.1.37
- UniProt
- P05132
- Ligands
- ADP, ATP, MG, PO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) | protein | 342 | 36% helix, 15% strand | P05132 |
| I | Camp-dependent protein kinase inhibitor, alpha form | protein | 20 | 30% helix, 10% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains E, I
- ATP · Adenosine-5'-triphosphate · ligand · chains E, I
- MG · Magnesium ion · metal · 2 copies · chains E
- PO4 · Phosphate ion · ion · chains E, I
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains E
- GOL · Glycerol · additive · chains E
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 | 158 | 0.79 | 0.95 | 34 | PO4, MG, ADP, ATP |
| 2 | 90 | 0.47 | 0.80 | 13 | MRD |
| 3 | 92 | 0.37 | 0.76 | 20 | empty |
| 4 | 93 | 0.35 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- E–I · 1032 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1RDQ · Hydrolysis of ATP in the crystal of Y204A mutant of cAMP-dependent protein kinase · the same entry in another collection · chain E against E, 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 1RDQ · PDBe 1RDQ · UniProt P05132
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