Research workbench
Crystal structure of the protein kinase CK2 catalytic domain from plasmodium falciparum bound to ATP
Analyse Crystal structure of the protein kinase CK2 catalytic domain from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVU
- Type
- protein
- Length
- 963 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase 2, alpha subunit
- EC
- 2.7.11.1
- UniProt
- Q8IIR9
- Ligands
- ATP, SO4, CL
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Casein kinase 2, alpha subunit (EC 2.7.11.1) | protein | 321 | 37% helix, 16% strand | Q8IIR9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.79 | 0.85 | 58 | ATP, SO4 |
| 2 | 62 | 0.68 | 0.95 | 19 | empty |
| 3 | 408 | 0.68 | 0.80 | 38 | EDO |
| 4 | 437 | 0.68 | 0.79 | 47 | ATP |
| 5 | 431 | 0.67 | 0.79 | 37 | ATP |
Interfaces
3 interfaces between chains.
- A–B · 827 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XVU · Crystal structure of the protein kinase CK2 catalytic domain from Plasmodium falciparum… · 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 Q8IIR9
- Elsewhere: RCSB PDB 5XVU · PDBe 5XVU · UniProt Q8IIR9
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