MolNFT v1 · #123660 · protein
Crystal structure of an acrdys heterodimer [RIA(92-365):C] of PKA
5JR7 · Camp-dependent protein kinase catalytic subunit alpha: “Crystal structure of an acrdys heterodimer [RIA(92-365):C] of PKA”. X-ray diffraction, 1 ligand (ADP), 17 pockets (best druggability 0.83). MolNFT v1 #123660 on GenesisL1: 3D…
- PDB
- 5JR7
- Type
- protein
- Length
- 1,209 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase type…
- EC
- 2.7.11.11
- UniProt
- P05132, P00514
- Ligands
- ADP
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 338 | 37% helix, 16% strand | P05132 |
| B | Camp-dependent protein kinase type I-alpha regulatory subunit | protein | 267 | 31% helix, 34% strand | P00514 |
| D | Camp-dependent protein kinase type I-alpha regulatory subunit | protein | 266 | 29% helix, 32% strand | P00514 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.83 | 0.92 | 44 | ADP |
| 2 | 1111 | 0.81 | 0.82 | 115 | ADP |
| 3 | 1158 | 0.76 | 0.78 | 84 | empty |
| 4 | 814 | 0.74 | 0.79 | 62 | empty |
| 5 | 250 | 0.58 | 0.79 | 36 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1961 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1885 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 530 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 5JR7 · Crystal structure of an ACRDYS heterodimer [RIa(92-365):C] of PKA · the same entry in another collection · chain C against C, TM-score 1.00
- P00514 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase type I-alpha… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P00514
- Elsewhere: RCSB PDB 5JR7 · PDBe 5JR7 · UniProt P05132 · UniProt P00514
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