Research workbench
Human CK2 catalytic domain in complex with a difurane derivative inhibitor (cpa)
Analyse Human CK2 catalytic domain in complex with a difurane derivative inhibitor (cpa) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MB6
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- 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
- 01I, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 329 | 39% helix, 15% strand | P68400 |
Ligands and binding sites
- 01I · naphtho[2,1-b:7,6-b']difuran-2,8-dicarboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.69 | 0.81 | 39 | 01I |
| 2 | 50 | 0.33 | 0.77 | 15 | empty |
| 3 | 52 | 0.30 | 0.76 | 13 | empty |
| 4 | 50 | 0.29 | 0.76 | 15 | SO4 |
Compared structures
- 3MB6 · Human CK2 catalytic domain in complex with a difurane derivative inhibitor (CPA) · 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 0.98
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 3MB6 · PDBe 3MB6 · UniProt P68400
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