Research workbench
Crystal structure of CK2ALPHA with N-((2-chloro-[1,1'-biphenyl]-4-yl) METHYL)BUTANE-1,4-diamine bound
Analyse Crystal structure of CK2ALPHA with N-((2-chloro-[1,1'-biphenyl]-4-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MMR
- Type
- protein
- Length
- 651 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
- H83, PO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 326 | 40% helix, 16% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 325 | 38% helix, 16% strand | P68400 |
Ligands and binding sites
- H83 · ~{N}'-[(3-chloranyl-4-phenyl-phenyl)methyl]butane-1,4-diamine · ligand · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- ACT · Acetate ion · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.75 | 0.82 | 70 | H83, ACT |
| 2 | 505 | 0.68 | 0.79 | 45 | empty |
| 3 | 104 | 0.67 | 0.90 | 21 | empty |
| 4 | 621 | 0.66 | 0.76 | 53 | empty |
| 5 | 108 | 0.43 | 0.77 | 19 | H83 |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5MMR · Crystal Structure of CK2alpha with N-((2-chloro-[1,1'-biphenyl]-4-yl)methyl)butane-1,4-dia… · 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 0.99
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 5MMR · PDBe 5MMR · UniProt P68400
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