Research workbench
Joint X-RAY/NEUTRON structure of pkac with products SR2-ADP and phosphorylated peptide SP20
Analyse Joint X-RAY/NEUTRON structure of pkac with products SR2-ADP and phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E21
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction; neutron diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; PSP20
- EC
- 2.7.11.11
- UniProt
- P05132
- Ligands
- ADP, SR
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction; neutron diffraction · 2 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 336 | 36% helix, 16% strand | P05132 |
| B | PSP20 | protein | 20 | 30% helix, 5% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- SR · Strontium ion · metal · 2 copies · chains A, B
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 | 272 | 0.81 | 0.92 | 41 | SR, ADP |
| 2 | 88 | 0.43 | 0.78 | 12 | empty |
| 3 | 111 | 0.42 | 0.77 | 20 | empty |
| 4 | 70 | 0.31 | 0.74 | 14 | empty |
| 5 | 53 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1055 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6E21 · Joint X-ray/neutron structure of PKAc with products Sr2-ADP and phosphorylated peptide… · 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 6E21 · PDBe 6E21 · UniProt P05132
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