Research workbench
Crystal structure of full-length symmetric CK2 holoenzyme
Analyse Crystal structure of full-length symmetric CK2 holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MD7
- Type
- protein
- Length
- 2,112 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 0.74
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit beta | protein | 199 | 47% 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 | 46% helix, 9% strand | P67870 |
| E, F, G | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 38% helix, 15% strand | P68400 |
| H | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 330 | 38% 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 | 856 | 0.74 | 0.79 | 79 | empty |
| 2 | 470 | 0.72 | 0.82 | 49 | empty |
| 3 | 500 | 0.72 | 0.81 | 54 | empty |
| 4 | 479 | 0.72 | 0.81 | 53 | empty |
| 5 | 448 | 0.71 | 0.82 | 50 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1940 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1911 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 679 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 644 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 636 Ų buried · 4 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 P67870
- Every structure of UniProt P68400
- Elsewhere: RCSB PDB 4MD7 · PDBe 4MD7 · UniProt P67870 · UniProt P68400
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