Research workbench
Crystal structure of the CK2 tetrameric holoenzyme
Analyse Crystal structure of the CK2 tetrameric holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DGL
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit beta; Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P67870, P68400
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit beta | protein | 200 | 40% helix, 10% strand | P67870 |
| B | Casein kinase II subunit beta | protein | 201 | 44% helix, 9% strand | P67870 |
| C | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 334 | 42% helix, 15% strand | P68400 |
| D | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 328 | 39% helix, 16% strand | P68400 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.74 | 0.80 | 65 | empty |
| 2 | 550 | 0.74 | 0.82 | 58 | empty |
| 3 | 124 | 0.69 | 0.90 | 21 | empty |
| 4 | 328 | 0.66 | 0.81 | 36 | empty |
| 5 | 301 | 0.66 | 0.81 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1975 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 659 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 630 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4DGL · Crystal Structure of the CK2 Tetrameric Holoenzyme · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.99
- P67870 · AlphaFold monomer V2.0 prediction for casein kinase II subunit beta (P67870) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P67870
- Every structure of UniProt P68400
- Elsewhere: RCSB PDB 4DGL · PDBe 4DGL · UniProt P67870 · UniProt P68400
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