5LQF: CDK1/CyclinB1/CKS2

CDK1/CyclinB1/CKS2 in complex with NU6102. Determined by X-ray diffraction at 2.06 Å resolution. Released 11 Jan 2017.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,580
Mol. weight: 153.23 kDa
Ligands: 4SP
Released: 11 Jan 2017

Explore 5LQF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LQF contains 81 α-helices and 34 β-strands across 6 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-12	9	1
β-strand	17-23	7	1
β-strand	29-34	6	1
α-helix	40-42	3
α-helix	46-57	12
β-strand	63	1	2
α-helix	64-65	2
β-strand	66-72	7	1
β-strand	75-81	7	1
α-helix	82-83	2
β-strand	85-86	2	2
α-helix	87-92	6
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	249-251	3
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-281	4
α-helix	285-288	4

Chain B: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	171-184	14
α-helix	199-216	18
α-helix	220-234	15
α-helix	241-243	3
α-helix	244-259	16
α-helix	263-265	3
α-helix	266-272	7
α-helix	279-292	14
α-helix	302-312	11
α-helix	317-330	14
α-helix	334-336	3
α-helix	341-356	16
α-helix	363-369	7
α-helix	373-391	19
α-helix	399-403	5
α-helix	407-409	3
α-helix	412-414	3
α-helix	416-419	4
α-helix	421-428	8

Chain C: 4 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	26-29	4
α-helix	37-39	3
α-helix	40-45	6
β-strand	55-59	5	4
β-strand	66-72	7	4

Chain D: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-12	9	5
β-strand	17-23	7	5
β-strand	29-34	6	5
α-helix	46-57	12
β-strand	63	1	6
α-helix	64-65	2
β-strand	66-72	7	5
β-strand	75-81	7	5
β-strand	85-86	2	6
α-helix	87-93	7
α-helix	95	1
α-helix	102-120	19
β-strand	124-125	2	7
α-helix	131-133	3
β-strand	134-136	3	6
β-strand	142-144	3	6
β-strand	151-152	2	7
β-strand	155-156	2	7
α-helix	172-175	4
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	249-251	3
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-281	4
α-helix	285-288	4

Chain E: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	171-184	14
α-helix	199-216	18
α-helix	220-236	17
α-helix	241-243	3
α-helix	244-259	16
α-helix	263-265	3
α-helix	266-271	6
α-helix	279-292	14
α-helix	302-312	11
α-helix	317-329	13
α-helix	330-332	3
α-helix	334-336	3
α-helix	341-355	15
α-helix	363-369	7
α-helix	373-391	19
α-helix	399-403	5
α-helix	407-409	3
α-helix	412-414	3
α-helix	416-419	4
α-helix	421-428	8

Chain F: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	8
α-helix	9-11	3
β-strand	12-13	2	8
β-strand	17-23	7	8
α-helix	26-29	4
α-helix	37-39	3
α-helix	40-45	6
β-strand	55-58	4	8
β-strand	66-72	7	8

Molecules and chains

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

Sequence of entity 1 (A, D), FASTA

>5LQF_1 Cyclin-dependent kinase 1 (chains A, D)
GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLL
KELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQG
IVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVL
LGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQ
DYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIK
KM

Sequence of entity 2 (B, E), FASTA

>5LQF_2 G2/mitotic-specific cyclin-B1 (chains B, E)
GSHMNLSSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQ
ETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKH
QIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFP
PSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTV
KNKYATSKHAKISTLPQLNSALVQDLAKAVAKV

Sequence of entity 3 (C, F), FASTA

>5LQF_3 Cyclin-dependent kinases regulatory subunit 2 (chains C, F)
GPLGSMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWV
HYMIHEPEPHILLFRRPLPKDQQK

Ligands and cofactors

ID	Name	Formula	Copies
4SP	O6-cyclohexylmethoxy-2-(4'-sulphamoylanilino) purine	C18 H22 N6 O3 S	2

Primary citation

Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines. Coxon, C.R., Anscombe, E., Harnor, S.J. et al. J Med Chem (2017) 60:1746-1767. DOI 10.1021/acs.jmedchem.6b01254 · 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
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
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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