MolNFT v1 · #173230 · protein
Structure of protein kinase CK2 catalytic subunit (CSNK2A1 gene product) in complex with the bivalent inhibitor KN2
7AT5 · Casein kinase II subunit alpha: “Structure of protein kinase CK2 catalytic subunit (CSNK2A1 gene product) in complex with the bivalent…”. X-ray diffraction, 3 ligands (RXE, 42J, SO4), 7 pockets (best druggability 0.72). MolNFT v1…
- 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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