6GZM: Human CKIdelta with A86

Crystal Structure of Human CKIdelta with A86. Determined by X-ray diffraction at 1.59 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,063
Mol. weight: 69.87 kDa
Ligands: CIT, LCI
Released: 29 Aug 2018

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

Secondary structure: helices and β-sheets

6GZM contains 35 α-helices and 27 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	1
β-strand	21-24	4	1
β-strand	27-28	2	2
β-strand	33-34	2	2
β-strand	37-41	5	1
α-helix	49-58	10
α-helix	66-67	2
β-strand	68-74	7	1
β-strand	77-82	6	1
β-strand	88	1	3
α-helix	89-95	7
α-helix	102-121	20
β-strand	124-125	2	4
α-helix	131-133	3
β-strand	134-136	3	3
α-helix	139-141	3
α-helix	144	1
β-strand	145-147	3	3
β-strand	154-155	2	4
β-strand	157	1	5
α-helix	163	1
β-strand	164	1	5
α-helix	165-167	3
α-helix	171-173	3
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	266-279	14
α-helix	289-292	4

Chain B: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	6
β-strand	9-18	10	6
β-strand	21-28	8	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	137	1
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	177-179	3
α-helix	182-185	4
α-helix	192-208	17
α-helix	221-233	13
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Casein kinase I isoform delta	A, B	protein	295	Homo sapiens	P48730 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GZM_1 Casein kinase I isoform delta (chains A, B)
MELRVGNRYRLGNKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQ
GGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIH
SKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYA
SINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVL
CKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKF

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
LCI	[4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl…	C18 H26 F N6	2

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

Primary citation

Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models. Minzel, W., Venkatachalam, A., Fink, A. et al. Cell (2018) 175:171-185.e25. DOI 10.1016/j.cell.2018.07.045 · 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)
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
4TWC 1.7 Å, 2-Benzamido-N-(1H-benzo[d]imidazol-2-yl)thiazole-4- carboxamide derivatives as potent…

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