8D7N: Human Casein kinase 1 delta

Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide. Determined by X-ray diffraction at 1.66 Å resolution. Released 17 May 2023.

Method: X-ray diffraction
Resolution: 1.66 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,381
Mol. weight: 72.75 kDa
Released: 17 May 2023

Explore 8D7N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D7N contains 34 α-helices and 30 β-strands across 4 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-18	10	1
β-strand	21-28	8	1
β-strand	34-41	8	1
α-helix	49-59	11
α-helix	66-67	2
β-strand	68-74	7	1
β-strand	77-83	7	1
β-strand	88	1	2
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	3
α-helix	131-133	3
β-strand	134-136	3	2
α-helix	139-143	5
β-strand	145-147	3	2
β-strand	154-155	2	3
β-strand	157	1	4
α-helix	163	1
β-strand	164	1	4
α-helix	165-167	3
α-helix	171-173	3
β-strand	175	1	5
α-helix	182-185	4
α-helix	188-190	3
α-helix	192-208	17
α-helix	221-234	14
α-helix	237-240	4
α-helix	246-257	12
α-helix	262-264	3
α-helix	266-279	14

Chain B: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	9-18	10	6
β-strand	21-28	8	6
β-strand	34-41	8	6
α-helix	49-58	10
α-helix	66-67	2
β-strand	68-74	7	6
β-strand	77-83	7	6
β-strand	88	1	7
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	8
α-helix	131-133	3
β-strand	134-136	3	7
α-helix	139-141	3
β-strand	145-147	3	7
β-strand	154-155	2	8
β-strand	157	1	9
α-helix	163	1
β-strand	164	1	9
α-helix	165-167	3
α-helix	171-173	3
β-strand	175	1	10
α-helix	182-185	4
α-helix	188-190	3
α-helix	192-208	17
α-helix	221-234	14
α-helix	237-240	4
α-helix	246-257	12
α-helix	262-264	3
α-helix	266-280	15

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	666	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase I isoform delta	A, B	protein	301	Homo sapiens	P48730 (AlphaFold model)
Period circadian protein homolog 2 peptide	C, D	protein	12	Homo sapiens	O15055 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8D7N_1 Casein kinase I isoform delta (chains A, B)
GAMDPEFMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIES
KIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMI
SRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNL
TGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKM
STPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNML
K

Sequence of entity 2 (C, D), FASTA

>8D7N_2 Period circadian protein homolog 2 peptide (chains C, D)
GKAESVASLTSQ

Primary citation

PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period. Philpott, J.M., Freeberg, A.M., Park, J. et al. Mol Cell (2023) 83:1677-1692.e8. DOI 10.1016/j.molcel.2023.04.019 · PubMed

Other PDB entries of the same protein (UniProt P48730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SIX 1.23 Å, CK1d in complex with IG130
6RCG 1.4 Å, Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor
6RCH 1.45 Å, Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133…
8IZC 1.45 Å, Human CK1 Delta Kinase structure bound to Inhibitor
9SIV 1.5 Å, Phosphorylated CK1d in complex with IG84
9SIZ 1.5 Å, CK1d in complex with IG138
9SIW 1.55 Å, CK1d in complex with IG111
6PXN 1.55 Å, Human Casein Kinase 1 delta Tau mutant (R178C)
6GZM 1.59 Å, Crystal Structure of Human CKIdelta with A86
9SJ1 1.6 Å, CK1d in complex with IG84
8D7O 1.65 Å, Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide
4TWC 1.7 Å, 2-Benzamido-N-(1H-benzo[d]imidazol-2-yl)thiazole-4- carboxamide derivatives as potent…

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