6YZH: P8C9

Crystal structure of P8C9 bound to CK2alpha. Determined by X-ray diffraction at 1.19 Å resolution. Released 19 May 2021.

Method: X-ray diffraction
Resolution: 1.19 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,481
Mol. weight: 48.47 kDa
Ligands: ADP, MG
Released: 19 May 2021

Explore 6YZH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YZH contains 27 α-helices and 14 β-strands across 2 chains. 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: 27 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	-26--23	4	1
α-helix	4-6	3
α-helix	21-24	4
α-helix	26-28	3
β-strand	29-32	4	1
α-helix	36-38	3
β-strand	39-47	9	2
β-strand	51-58	8	2
β-strand	63-70	8	2
α-helix	71	1
α-helix	75-88	14
β-strand	94	1	3
α-helix	95-96	2
β-strand	97-102	6	2
β-strand	109-114	6	2
α-helix	121-124	4
α-helix	125-127	3
α-helix	130-149	20
β-strand	152-153	2	4
α-helix	159-161	3
β-strand	162-165	4	3
α-helix	166-168	3
β-strand	170-173	4	3
β-strand	180-181	2	4
α-helix	195-197	3
α-helix	200-203	4
α-helix	212-227	16
α-helix	238-249	12
α-helix	252-260	9
α-helix	269-272	4
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	325-330	6

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	97-98	2	2
β-strand	101-102	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase II subunit alpha	A	protein	398	Homo sapiens	P68400 (AlphaFold model)
P8C9	D	protein	10	Homo sapiens

Sequence of entity 1 (A), FASTA

>6YZH_1 Casein kinase II subunit alpha (chains A)
MNTIHHHHHHNTSGSGGGGGRLVPRGSMSENLYFQGSMDIEFGEGEGSEGPVPSRARVYT
DVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPV
KKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDI
RFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVA
SRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTED
LYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRL
TAREAMEHPYFYTVVKENLYFQGSSGSGSGSSHHHHHH

Sequence of entity 2 (D), FASTA

>6YZH_2 P8C9 (chains D)
AARLYGFKWX

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL, NA) are not listed.

Primary citation

Development of small cyclic peptides targeting the CK2 alpha / beta interface. Atkinson, E.L., Iegre, J., D'Amore, C. et al. Chem Commun (Camb) (2022) 58:4791-4794. DOI 10.1039/d2cc00707j · 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
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
4KWP 1.25 Å, Crystal Structure of Human CK2-alpha in complex with a benzimidazole inhibitor (K164) at…
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

Browse structure collections

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