Research workbench
Crystal structure of a heterotetrameric CK2 holoenzyme complex carrying the andante-mutation in CK2BETA and consistent with proposed models of autoinhibition and trans-autophosphorylation
Analyse Crystal structure of a heterotetrameric CK2 holoenzyme complex carrying the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NH1
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha; Casein kinase II subunit beta
- EC
- 2.7.11.1
- UniProt
- P68400, P67870
- Ligands
- ACP, MG, ZN
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 330 | 36% helix, 15% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 37% helix, 15% strand | P68400 |
| C, D | Casein kinase II subunit beta | protein | 201 | 42% helix, 10% strand | P67870 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.73 | 0.82 | 56 | empty |
| 2 | 458 | 0.71 | 0.81 | 56 | empty |
| 3 | 55 | 0.69 | 0.97 | 20 | empty |
| 4 | 53 | 0.68 | 0.96 | 18 | empty |
| 5 | 453 | 0.67 | 0.79 | 58 | MG, ACP |
Interfaces
5 interfaces between chains.
- C–D · 1957 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 658 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 446 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 444 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4NH1 · Crystal structure of a heterotetrameric CK2 holoenzyme complex carrying the… · 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 A 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 D 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 P68400
- Every structure of UniProt P67870
- Elsewhere: RCSB PDB 4NH1 · PDBe 4NH1 · UniProt P68400 · UniProt P67870
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