4Y72: Human CDK1/CyclinB1/CKS2 With Inhibitor

Human CDK1/CyclinB1/CKS2 With Inhibitor. Determined by X-ray diffraction at 2.3 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,551
Mol. weight: 76.57 kDa
Ligands: LZ9
Released: 12 Aug 2015

Explore 4Y72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y72 contains 40 α-helices and 17 β-strands across 3 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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-12	9	1
β-strand	16-23	8	1
β-strand	29-36	8	1
α-helix	46-55	10
β-strand	63	1	2
β-strand	66-71	6	1
β-strand	75-81	7	1
β-strand	85-86	2	2
α-helix	87-93	7
α-helix	95	1
α-helix	102-120	19
β-strand	124-125	2	3
α-helix	131-133	3
β-strand	134-136	3	2
β-strand	142-144	3	2
β-strand	151-152	2	3
β-strand	155-156	2	3
α-helix	172-175	4
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	244-246	3
α-helix	250-252	3
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-282	5
α-helix	285-287	3

Chain B: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	170-183	14
α-helix	198-214	17
α-helix	219-234	16
α-helix	240-242	3
α-helix	243-258	16
α-helix	262-264	3
α-helix	265-271	7
α-helix	278-291	14
α-helix	301-311	11
α-helix	316-329	14
α-helix	333-335	3
α-helix	340-354	15
α-helix	362-368	7
α-helix	372-390	19
α-helix	398-402	5
α-helix	406-408	3
α-helix	411-413	3
α-helix	415-418	4
α-helix	420-427	8

Chain C: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	4
α-helix	9-11	3
β-strand	12-13	2	4
β-strand	17-23	7	4
α-helix	24-25	2
α-helix	26-29	4
α-helix	37-39	3
α-helix	40-46	7
β-strand	55-58	4	4
β-strand	66-72	7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 1	A	protein	302	Homo sapiens	P06493 (AlphaFold model)
G2/mitotic-specific cyclin-B1	B	protein	273	Homo sapiens	P14635 (AlphaFold model)
Cyclin-dependent kinases regulatory subunit 2	C	protein	84	Homo sapiens	P33552 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4Y72_1 Cyclin-dependent kinase 1 (chains A)
GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLL
KELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQG
IVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVL
LGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQ
DYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIK
KM

Sequence of entity 2 (B), FASTA

>4Y72_2 G2/mitotic-specific cyclin-B1 (chains B)
GSHMNLSSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQ
ETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKH
QIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFP
PSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTV
KNKYATSKHAKISTLPQLNSALVQDLAKAVAKV

Sequence of entity 3 (C), FASTA

>4Y72_3 Cyclin-dependent kinases regulatory subunit 2 (chains C)
GPLGSMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWV
HYMIHEPEPHILLFRRPLPKDQQK

Ligands and cofactors

ID	Name	Formula	Copies
LZ9	{[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxam…	C17 H11 F3 N4 O2	1

Primary citation

CDK1 structures reveal conserved and unique features of the essential cell cycle CDK. Brown, N.R., Korolchuk, S., Martin, M.P. et al. Nat Commun (2015) 6:6769-6769. DOI 10.1038/ncomms7769 · 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)
5HQ0 2.3 Å, Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor
6GU6 2.33 Å, CDK1/Cks2 in complex with Dinaciclib
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

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