MolNFT v1 · #173703 · protein
Tetragonal structure of human protein kinase CK2 catalytic subunit in complex with a heparin oligo saccharide
7B8I · Casein kinase II subunit alpha: “Tetragonal structure of human protein kinase CK2 catalytic subunit in complex with a heparin oligo saccharide”. X-ray diffraction, 3 ligands (IDS, SGN, SO4), 5 pockets (best druggability 0.71).…
- PDB
- 7B8I
- Type
- protein
- Length
- 664 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
- IDS, SGN, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 41% helix, 16% strand | P68400 |
Ligands and binding sites
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 4 copies · chains A, B
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.71 | 0.83 | 44 | empty |
| 2 | 474 | 0.71 | 0.81 | 57 | SO4 |
| 3 | 474 | 0.60 | 0.74 | 47 | SO4 |
| 4 | 60 | 0.33 | 0.77 | 13 | empty |
| 5 | 53 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7B8I · Tetragonal structure of human protein kinase CK2 catalytic subunit in complex with a… · 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 A 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 7B8I · PDBe 7B8I · UniProt P68400
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