MolNFT v1 · #151042 · protein
High-salt structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA/CSKN2A1 gene product) in complex with the indenoindole-type inhibitor THN27
6HBN · Casein kinase II subunit alpha: “High-salt structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA/CSKN2A1 gene product) in…”. X-ray diffraction, 3 ligands (FXB, NA, CL), 5 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6HBN
- 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
- FXB, NA, CL
- Pockets
- 5 · best druggability 0.86
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
- 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 · 3 copies · chains A, B
- CL · Chloride ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.86 | 0.90 | 77 | empty |
| 2 | 293 | 0.73 | 0.86 | 43 | empty |
| 3 | 277 | 0.70 | 0.84 | 40 | FXB |
| 4 | 382 | 0.70 | 0.82 | 50 | CL, FXB |
| 5 | 51 | 0.25 | 0.73 | 18 | CL |
Interfaces
1 interface between chains.
- A–B · 1161 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6HBN · High-salt structure of protein kinase CK2 catalytic subunit (isoform CK2ALPHA/CSKN2A1… · 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 0.97
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 6HBN · PDBe 6HBN · UniProt P68400
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