MolNFT v1 · #126512 · protein
Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2ALPHA') with the inhibitor 4'-carboxy-6,8-chloro- flavonol (FLC21)
5M56 · Casein kinase II subunit alpha': “Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2ALPHA') with the…”. X-ray diffraction, 2 ligands (7FC, CL), 7 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5M56
- Type
- protein
- Length
- 659 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
- P19784
- Ligands
- 7FC, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha' (EC 2.7.11.1) | protein | 331 | 40% helix, 15% strand | P19784 |
| B | Casein kinase II subunit alpha' (EC 2.7.11.1) | protein | 328 | 41% helix, 14% strand | P19784 |
Ligands and binding sites
- 7FC · 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.80 | 0.84 | 84 | 7FC, GOL |
| 2 | 102 | 0.42 | 0.78 | 24 | empty |
| 3 | 85 | 0.35 | 0.75 | 17 | empty |
| 4 | 82 | 0.35 | 0.75 | 17 | empty |
| 5 | 84 | 0.34 | 0.75 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5M56 · Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform… · the same entry in another collection · chain B against B, TM-score 1.00
- P19784 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha' (P19784) · 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 P19784
- Elsewhere: RCSB PDB 5M56 · PDBe 5M56 · UniProt P19784
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