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Structure of protein kinase CK2 catalytic subunit with the CK2BETA- competitive bisubstrate inhibitor ARC3140
Analyse Structure of protein kinase CK2 catalytic subunit with the CK2BETA- competitive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SPW
- Type
- protein
- Length
- 348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha; ARC3140
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- A0Z, NA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 327 | 44% helix, 15% strand | P68400 |
| B, C, D | ARC3140 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- A0Z · 8-[4,5,6,7-tetrakis(iodanyl)benzimidazol-1-yl]octanoic acid · ligand · 3 copies · chains A, B, C, D
- NA · Sodium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.73 | 0.83 | 43 | A0Z |
| 2 | 139 | 0.41 | 0.74 | 24 | empty |
| 3 | 78 | 0.37 | 0.77 | 15 | A0Z |
| 4 | 51 | 0.34 | 0.78 | 16 | empty |
| 5 | 53 | 0.29 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 618 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 204 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 d-amino (covalent ligand, D-amino acid).
Compared structures
- 6SPW · Structure of protein kinase CK2 catalytic subunit with the CK2beta-competitive… · 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 6SPW · PDBe 6SPW · UniProt P68400
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