Research workbench
Crystal structure of the catalytic subunit of camp-dependent protein kinase displaying partial phosphoryl transfer of AMP-pnp onto a substrate peptide
Analyse Crystal structure of the catalytic subunit of camp-dependent protein kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HPU
- Type
- protein
- Length
- 358 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
- P05132, P63248
- Ligands
- ANP, MYR, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 339 | 37% helix, 16% strand | P05132 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 19 | 32% helix, 5% strand | P63248 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains E, I
- MYR · Myristic acid · ligand · chains E
- MG · Magnesium ion · metal · 2 copies · chains E, I
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 | 217 | 0.80 | 0.94 | 36 | ANP, MG |
| 2 | 77 | 0.47 | 0.82 | 13 | MYR |
| 3 | 78 | 0.43 | 0.80 | 17 | empty |
| 4 | 134 | 0.40 | 0.75 | 31 | empty |
| 5 | 68 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- E–I · 1058 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent (phosphorylation, covalent ligand).
Compared structures
- 4HPU · Crystal structure of the catalytic subunit of cAMP-dependent protein kinase displaying… · the same entry in another collection · chain E against E, 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 I against A, TM-score 0.42
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 4HPU · PDBe 4HPU · UniProt P05132 · UniProt P63248
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