Research workbench
Crystal structure of CK2ALPHA with ZT0432 bound
Analyse Crystal structure of CK2ALPHA with ZT0432 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MP8
- Type
- protein
- Length
- 648 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
- ADP, RKN, MG, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 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 | 325 | 40% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 323 | 41% helix, 16% strand | P68400 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- RKN · (3-chloranyl-4-phenyl-phenyl)methyl-methyl-azanium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.76 | 0.84 | 64 | ADP, RKN, MG |
| 2 | 116 | 0.74 | 0.94 | 22 | RKN |
| 3 | 356 | 0.70 | 0.82 | 37 | ADP |
| 4 | 523 | 0.65 | 0.77 | 39 | empty |
| 5 | 174 | 0.43 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 5MP8 · PDBe 5MP8 · UniProt P68400
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