6GU6: CDK1/Cks2

CDK1/Cks2 in complex with Dinaciclib. Determined by X-ray diffraction at 2.33 Å resolution. Released 5 Dec 2018.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,058
Mol. weight: 45.24 kDa
Ligands: 1QK
Released: 5 Dec 2018

Explore 6GU6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GU6 contains 21 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: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
β-strand	16-23	8	1
β-strand	29-36	8	1
α-helix	37-39	3
α-helix	48-57	10
β-strand	63	1	2
β-strand	66-72	7	1
β-strand	75-81	7	1
β-strand	85-86	2	2
α-helix	87-92	6
α-helix	95	1
α-helix	102-120	19
α-helix	131-133	3
β-strand	134-136	3	2
β-strand	142-144	3	2
α-helix	149-152	4
α-helix	164-167	4
α-helix	172-175	4
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	250-252	3
α-helix	258-267	10
α-helix	272-274	3
α-helix	276-277	2
α-helix	278-282	5
α-helix	285-287	3

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	3
α-helix	9-11	3
β-strand	12-13	2	3
β-strand	17-23	7	3
α-helix	26-31	6
α-helix	40-45	6
β-strand	55-58	4	3
β-strand	66-72	7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 1	A	protein	302	Homo sapiens	P06493 (AlphaFold model)
Cyclin-dependent kinases regulatory subunit 2	B	protein	84	Homo sapiens	P33552 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GU6_1 Cyclin-dependent kinase 1 (chains A)
GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLL
KELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQG
IVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVL
LGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQ
DYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIK
KM

Sequence of entity 2 (B), FASTA

>6GU6_2 Cyclin-dependent kinases regulatory subunit 2 (chains B)
GPLGSMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWV
HYMIHEPEPHILLFRRPLPKDQQK

Ligands and cofactors

ID	Name	Formula	Copies
1QK	3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-…	C21 H29 N6 O2	1

Primary citation

Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition. Wood, D.J., Korolchuk, S., Tatum, N.J. et al. Cell Chem Biol (2019) 26:121-130.e5. DOI 10.1016/j.chembiol.2018.10.015 · PubMed

Other PDB entries of the same protein (UniProt P06493 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GU2 2.0 Å, CDK1/CyclinB/Cks2 in complex with Flavopiridol
5LQF 2.06 Å, CDK1/CyclinB1/CKS2 in complex with NU6102
6TWN 2.28 Å, Crystal structure of Talin1 R7R8 in complex with CDK1 (206-223)
4Y72 2.3 Å, Human CDK1/CyclinB1/CKS2 With Inhibitor
5HQ0 2.3 Å, Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor
11GY 2.4 Å, Crystal structure of selective inhibitor 16 bound at the active site of CDK1
4YC6 2.6 Å, CDK1/CKS1
6GU3 2.65 Å, CDK1/CyclinB/Cks2 in complex with AZD5438
4YC3 2.7 Å, CDK1/CyclinB1/CKS2 Apo
6GU4 2.73 Å, CDK1/CyclinB/Cks2 in complex with CGP74514A
6GU7 2.75 Å, CDK1/Cks2 in complex with AZD5438
9SKQ 3.4 Å, Cryo-EM structure of CAK-CDK1-cyclin B1

Browse structure collections

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