Research workbench
Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole
Analyse Crystal structure of the catalytic subunit of human protein kinase CK2 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H30
- Type
- protein
- Length
- 666 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
- RFZ, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 333 | 41% helix, 15% strand | P68400 |
Ligands and binding sites
- RFZ · 5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole · ligand · 3 copies · chains A, B
- CL · Chloride ion · ion · 32 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.83 | 0.84 | 90 | CL |
| 2 | 656 | 0.73 | 0.80 | 54 | CL |
| 3 | 414 | 0.71 | 0.82 | 44 | RFZ, CL |
| 4 | 357 | 0.67 | 0.81 | 41 | RFZ, CL |
| 5 | 113 | 0.48 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1466 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3H30 · Crystal structure of the catalytic subunit of human protein kinase CK2 with… · the same entry in another collection · chain B against B, 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 0.97
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 3H30 · PDBe 3H30 · UniProt P68400
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