MolNFT v1 · #124942 · protein

Crystal structure of CK2

5KU8 · Casein kinase II subunit alpha: “Crystal structure of CK2”. X-ray diffraction, 2 ligands (6XK, SO4), 7 pockets (best druggability 0.76). MolNFT v1 #124942 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KU8
Type: protein
Length: 659 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: 6XK, SO4
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Casein kinase II subunit alpha (EC 2.7.11.1)	protein	328	42% helix, 15% strand	P68400
B	Casein kinase II subunit alpha (EC 2.7.11.1)	protein	331	43% helix, 15% strand	P68400

Ligands and binding sites

6XK · ~{N}-[2-[(1~{S},2~{S})-2-(aminomethyl)cyclopropyl]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 12 copies · chains A, B
EDO · 1,2-ethanediol · additive · 27 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	653	0.76	0.82	75	SO4, EDO, 6XK
2	252	0.69	0.85	30	empty
3	469	0.68	0.79	50	EDO, 6XK
4	169	0.49	0.77	24	empty
5	61	0.36	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 583 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5KU8 · 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 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 5KU8 · PDBe 5KU8 · UniProt P68400

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