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Structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA') in complex with the indenoindole-type inhibitor 4P
Analyse Structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA') in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OOI
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.998
- Source
- Homo sapiens
- Molecule
- Casein kinase II subunit alpha'
- EC
- 2.7.11.1
- UniProt
- P19784
- Ligands
- 9YE, NA
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.998 · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha' (EC 2.7.11.1) | protein | 329 | 41% helix, 16% strand | P19784 |
| B | Casein kinase II subunit alpha' (EC 2.7.11.1) | protein | 325 | 41% helix, 15% strand | P19784 |
Ligands and binding sites
- 9YE · 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.85 | 0.86 | 110 | NA |
| 2 | 149 | 0.70 | 0.89 | 24 | 9YE |
| 3 | 179 | 0.65 | 0.85 | 29 | 9YE |
| 4 | 61 | 0.43 | 0.82 | 16 | empty |
| 5 | 58 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5OOI · Structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA') in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P19784 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha' (P19784) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P19784
- Elsewhere: RCSB PDB 5OOI · PDBe 5OOI · UniProt P19784
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