MolNFT v1 · #134350 · protein

Crystal structure of CK2

5T1H · Casein kinase II subunit alpha: “Crystal structure of CK2”. X-ray diffraction, 2 ligands (75E, SO4), 7 pockets (best druggability 0.69). MolNFT v1 #134350 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5T1H
Type: protein
Length: 662 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: 75E, SO4
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Casein kinase II subunit alpha (EC 2.7.11.1)	protein	331	42% helix, 15% strand	P68400

Ligands and binding sites

75E · 7-(cyclopropylamino)-5-[3-(6-oxo-1,6-dihydropyridin-3-yl)thiophen-2-yl]pyrazolo[1,5-a]pyrimidine-3-carbonitrile · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 13 copies · chains A, B
EDO · 1,2-ethanediol · additive · 26 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.69	0.86	35	EDO
2	537	0.68	0.78	52	SO4, EDO, 75E
3	287	0.67	0.82	36	75E
4	305	0.64	0.80	34	SO4, EDO
5	93	0.44	0.79	19	empty

Interfaces

1 interface between chains.

A–B · 497 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5T1H · Crystal structure of CK2 · 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 1.00

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 5T1H · PDBe 5T1H · UniProt P68400

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