Research workbench
Crystal structure of maize CK2 in complex with the inhibitor apigenin
Analyse Crystal structure of maize CK2 in complex with the inhibitor apigenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DGM
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P28523
- Ligands
- AGI
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 326 | 44% helix, 15% strand | P28523 |
Ligands and binding sites
- AGI · 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.68 | 0.80 | 56 | AGI |
| 2 | 72 | 0.44 | 0.81 | 18 | EDO |
Compared structures
- 4DGM · Crystal Structure of maize CK2 in complex with the inhibitor apigenin · the same entry in another collection · chain A against A, TM-score 1.00
- P28523 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P28523) · 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 P28523
- Elsewhere: RCSB PDB 4DGM · PDBe 4DGM · UniProt P28523
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