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Crystal structure of CK2A2 form-2

Analyse Crystal structure of CK2A2 form-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YF9
Type: protein
Length: 638 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: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Casein kinase II subunit alpha' (EC 2.7.11.1)	protein	319	40% helix, 14% strand	P19784
B	Casein kinase II subunit alpha' (EC 2.7.11.1)	protein	319	41% helix, 14% strand	P19784

Ligands and binding sites

NIO · Nicotinic acid · ligand · 2 copies · chains X, B
SO4 · Sulfate ion · ion · 8 copies · chains X, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	947	0.83	0.84	103	NIO, SO4
2	121	0.57	0.83	21	NIO
3	53	0.32	0.77	12	SO4
4	70	0.32	0.74	14	SO4

Interfaces

1 interface between chains.

X–B · 834 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5YF9 · Crystal structure of CK2a2 form-2 · the same entry in another collection · chain X against X, TM-score 1.00
P19784 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha' (P19784) · 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 P19784
Elsewhere: RCSB PDB 5YF9 · PDBe 5YF9 · UniProt P19784

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