4KWP: Human CK2-alpha

Crystal Structure of Human CK2-alpha in complex with a benzimidazole inhibitor (K164) at 1.25 A resolution. Determined by X-ray diffraction at 1.25 Å resolution. Released 9 Apr 2014.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,363
Mol. weight: 41.61 kDa
Ligands: EXX
Released: 9 Apr 2014

Explore 4KWP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KWP contains 25 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	21-24	4
α-helix	26-28	3
α-helix	36-38	3
β-strand	39-47	9	1
β-strand	51-58	8	1
β-strand	63-70	8	1
α-helix	71	1
α-helix	75-88	14
β-strand	94	1	2
α-helix	95-96	2
β-strand	97-103	7	1
β-strand	108-114	7	1
α-helix	121-125	5
α-helix	130-149	20
β-strand	152-153	2	3
α-helix	159-161	3
β-strand	162-165	4	2
β-strand	170-173	4	2
β-strand	180-181	2	3
α-helix	195-197	3
α-helix	200-203	4
α-helix	212-226	15
α-helix	238-249	12
α-helix	251-260	10
α-helix	267-271	5
α-helix	277-280	4
α-helix	281-284	4
α-helix	290-292	3
α-helix	295-304	10
α-helix	309-311	3
α-helix	313-314	2
α-helix	315-319	5
α-helix	322-324	3
α-helix	328-329	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase II subunit alpha	A	protein	336	Homo sapiens	P68400 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4KWP_1 Casein kinase II subunit alpha (chains A)
MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINIT
NNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTD
FKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAE
FYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYD
QLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDF
LDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS

Ligands and cofactors

ID	Name	Formula	Copies
EXX	4,5,6,7-tetrabromo-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-1H-benzimidazole	C12 H10 Br4 N2 O3	1

Water and common crystallization additives (SO4, EDO, PGE, DMS, PEG) are not listed.

Primary citation

Cell-permeable dual inhibitors of protein kinases CK2 and PIM-1: structural features and pharmacological potential. Cozza, G., Girardi, C., Ranchio, A. et al. Cell Mol Life Sci (2014) 71:3173-3185. DOI 10.1007/s00018-013-1552-5 · PubMed

Other PDB entries of the same protein (UniProt P68400 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WAR 1.04 Å, Crystal structure of human CK2a
5ZN1 1.05 Å, X-ray structure of protein kinase ck2 alpha subunit in D2O
8AEC 1.09 Å, Structure of Compound 17 bound to CK2alpha
5ZN0 1.1 Å, Joint X-ray/neutron structure of protein kinase ck2 alpha subunit
7I7Y 1.15 Å, Crystal Structure of 30 bound to CK2a
6YZH 1.19 Å, Crystal structure of P8C9 bound to CK2alpha
5ZN2 1.2 Å, X-ray structure of protein kinase ck2 alpha subunit H148A mutant
7I8G 1.23 Å, Crystal Structure of 58f bound to CK2a
5CVG 1.25 Å, Crystal Structure of CK2alpha with a novel closed conformation of the aD loop
7I8P 1.25 Å, Crystal Structure of 21 bound to CK2a
7I8N 1.28 Å, Crystal Structure of 12 bound to CK2a
8AE7 1.28 Å, The strucuture of Compound 15 bound to CK2alpha

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