6RU8: Casein Kinase I delta

Crystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated p63 PAD3P peptide. Determined by X-ray diffraction at 1.92 Å resolution. Released 13 May 2020.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,612
Mol. weight: 146.34 kDa
Ligands: ADP
Released: 13 May 2020

Explore 6RU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RU8 contains 77 α-helices and 58 β-strands across 8 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-17	9	1
β-strand	22-28	7	1
β-strand	33-41	9	1
α-helix	49-58	10
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	139-141	3
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
α-helix	289-292	4

Chain B: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	9-17	9	6
β-strand	22-28	7	6
β-strand	33-41	9	6
α-helix	49-59	11
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
α-helix	144	1
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	247-257	11
α-helix	262-264	3
α-helix	266-279	14
α-helix	289-292	4

Chain C: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	11
β-strand	9-17	9	11
β-strand	22-28	7	11
β-strand	33-41	9	11
α-helix	49-59	11
α-helix	65-67	3
β-strand	68-74	7	11
β-strand	77-83	7	11
β-strand	88	1	12
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	13
α-helix	131-133	3
β-strand	134-136	3	12
α-helix	139-141	3
α-helix	144	1
β-strand	145-147	3	12
β-strand	154-155	2	13
α-helix	165-167	3
α-helix	171-173	3
β-strand	175	1	14
α-helix	182-185	4
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
α-helix	289-292	4

Chain D: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	15
β-strand	9-17	9	15
β-strand	22-28	7	15
β-strand	33-41	9	15
α-helix	49-59	11
α-helix	65-67	3
β-strand	68-74	7	15
β-strand	77-83	7	15
β-strand	88	1	16
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	17
α-helix	131-133	3
β-strand	134-136	3	16
α-helix	139-141	3
α-helix	144	1
β-strand	145-147	3	16
β-strand	154-155	2	17
β-strand	157	1	18
α-helix	163	1
β-strand	164	1	18
α-helix	165-167	3
α-helix	171-173	3
β-strand	175	1	19
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
α-helix	289-292	4

Chains E, F, G and H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	583-586	4
β-strand	589	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase I isoform delta	A, B, C, D	protein	296	Homo sapiens	P48730 (AlphaFold model)
Tumor protein 63	E, F, G, H	protein	12	Homo sapiens	Q9H3D4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6RU8_1 Casein kinase I isoform delta (chains A, B, C, D)
SMMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKM
MQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEY
IHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTAR
YASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIE
VLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK

Sequence of entity 2 (E, F, G, H), FASTA

>6RU8_2 Tumor protein 63 (chains E, F, G, H)
SSASTVSVGSSY

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4

Water and common crystallization additives (NA, SO4, EDO) are not listed.

Primary citation

p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Gebel, J., Tuppi, M., Chaikuad, A. et al. Nat Chem Biol (2020) 16:1078-1086. DOI 10.1038/s41589-020-0600-3 · 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
8D7N 1.66 Å, Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide

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