MolNFT v1 · #171276 · protein
Crystal structure of P8C9 bound to CK2ALPHA
6YZH · Casein kinase II subunit alpha: “Crystal structure of P8C9 bound to CK2ALPHA”. X-ray diffraction, 4 ligands (Q2E, ADP, MG), 2 pockets (best druggability 0.67). MolNFT v1 #171276 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6YZH
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha; P8C9
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- Q2E, ADP, MG, NA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 344 | 40% helix, 17% strand | P68400 |
| D | P8C9 | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- Q2E · (2~{S})-2-azanyl-3-(2-methylsulfanyl-1~{H}-indol-3-yl) propanal · ligand · chains A, D
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.67 | 0.79 | 41 | MG, ADP |
| 2 | 59 | 0.37 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 435 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 P68400
- Elsewhere: RCSB PDB 6YZH · PDBe 6YZH · UniProt P68400
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