MolNFT v1 · #140402 · protein
Crystal structure of CK2A2 form 3
5Y9M · Casein kinase II subunit alpha': “Crystal structure of CK2A2 form 3”. X-ray diffraction, 2 ligands (NIO, SO4), 8 pockets (best druggability 0.64). MolNFT v1 #140402 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y9M
- Type
- protein
- Length
- 639 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
- NIO, SO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Casein kinase II subunit alpha' (EC 2.7.11.1) | protein | 319 | 41% helix, 14% strand | P19784 |
| A | Casein kinase II subunit alpha' (EC 2.7.11.1) | protein | 320 | 43% helix, 14% strand | P19784 |
Ligands and binding sites
- NIO · Nicotinic acid · ligand · 2 copies · chains X, A
- SO4 · Sulfate ion · ion · 4 copies · chains X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.64 | 0.82 | 30 | NIO |
| 2 | 305 | 0.63 | 0.79 | 40 | NIO |
| 3 | 216 | 0.54 | 0.78 | 27 | empty |
| 4 | 171 | 0.48 | 0.76 | 21 | empty |
| 5 | 58 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- X–A · 425 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 5Y9M · PDBe 5Y9M · UniProt P19784
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