Research workbench
Crystal structure of full-length symmetric CK2 holoenzyme with mutated alpha subunit (F121E)
Analyse Crystal structure of full-length symmetric CK2 holoenzyme with mutated alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MD8
- Type
- protein
- Length
- 2,113 residues
- Chains
- 8
- 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
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit beta | protein | 199 | 48% helix, 9% strand | P67870 |
| B, D | Casein kinase II subunit beta | protein | 195 | 47% helix, 9% strand | P67870 |
| C | Casein kinase II subunit beta | protein | 197 | 48% helix, 9% strand | P67870 |
| E, F, G | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 39% helix, 15% strand | P68400 |
| H | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 331 | 39% helix, 15% strand | P68400 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.73 | 0.82 | 48 | empty |
| 2 | 492 | 0.72 | 0.81 | 56 | empty |
| 3 | 1010 | 0.71 | 0.75 | 71 | empty |
| 4 | 454 | 0.71 | 0.81 | 53 | empty |
| 5 | 453 | 0.71 | 0.81 | 52 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1946 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1910 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 642 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 640 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 630 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4MD8 · Crystal Structure of full-length symmetric CK2 holoenzyme with mutated alpha subunit… · the same entry in another collection · chain G against G, 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 E 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 P67870
- Every structure of UniProt P68400
- Elsewhere: RCSB PDB 4MD8 · PDBe 4MD8 · UniProt P67870 · UniProt P68400
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