Research workbench
LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA; CSNK2A1 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27
Analyse LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HME
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- FXB, NA, SO4, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.85 · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 43% helix, 15% strand | P68400 |
Ligands and binding sites
- FXB · 5-propan-2-yl-4-prop-2-enoxy-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.81 | 0.83 | 101 | SO4, FXB |
| 2 | 453 | 0.71 | 0.81 | 56 | SO4, FXB |
| 3 | 73 | 0.40 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 504 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HME · Low-salt structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA; CSNK2A1… · the same entry in another collection · chain A against A, 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 B 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 P68400
- Elsewhere: RCSB PDB 6HME · PDBe 6HME · UniProt P68400
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