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Structure of protein kinase CK2 catalytic subunit (CSNK2A1 gene product) in complex with the bivalent inhibitor KN2
Analyse Structure of protein kinase CK2 catalytic subunit (CSNK2A1 gene product) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AT5
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- RXE, 42J, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 43% helix, 15% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 331 | 43% helix, 15% strand | P68400 |
Ligands and binding sites
- RXE · ~{N}'-[2-(3,4-dichlorophenyl)ethyl]-~{N}-[4-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]butyl]butanediamide · ligand · 2 copies · chains A, B
- 42J · 2-(3,4-dichlorophenyl)ethanamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.72 | 0.83 | 38 | RXE |
| 2 | 69 | 0.71 | 0.95 | 16 | RXE |
| 3 | 419 | 0.69 | 0.81 | 46 | SO4, RXE |
| 4 | 138 | 0.65 | 0.87 | 23 | RXE |
| 5 | 219 | 0.59 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 439 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7AT5 · Structure of protein kinase ck2 catalytic subunit (csnk2a1 gene product) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain B 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 P68400
- Elsewhere: RCSB PDB 7AT5 · PDBe 7AT5 · UniProt P68400
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