Research workbench
Structures of the PKA ri alpha holoenzyme with the flhcc driver J-pkac alpha or native pkac alpha
Analyse Structures of the PKA ri alpha holoenzyme with the flhcc driver J-pkac alpha or… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BYR
- Type
- protein
- Length
- 1,386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnaj homolog subfamily B member 1,CAMP-dependent protein kinase catalytic subunit alpha…
- EC
- 2.7.11.11
- UniProt
- P25685, P17612, P00514
- Ligands
- ATP, MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dnaj homolog subfamily B member 1,CAMP-dependent protein kinase catalytic subunit alpha chimera (EC 2.7.11.11) | protein | 405 | 36% helix, 14% strand | P25685, P17612 |
| B, D | Camp-dependent protein kinase type I-alpha regulatory subunit | protein | 288 | 32% helix, 29% strand | P00514 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.81 | 0.94 | 37 | ATP, MG |
| 2 | 1138 | 0.80 | 0.82 | 104 | empty |
| 3 | 214 | 0.80 | 0.94 | 38 | ATP, MG |
| 4 | 666 | 0.77 | 0.83 | 63 | empty |
| 5 | 808 | 0.71 | 0.77 | 90 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2056 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2008 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1085 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 6BYR · Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native… · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.96
- P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.85
- P25685 · AlphaFold monomer V2.0 prediction for dnaj homolog subfamily B member 1 (P25685) · a predicted model of the same protein · chain A against A, TM-score 0.19
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 P25685
- Every structure of UniProt P17612
- Every structure of UniProt P00514
- Elsewhere: RCSB PDB 6BYR · PDBe 6BYR · UniProt P25685 · UniProt P17612 · UniProt P00514
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