6GU7: CDK1/Cks2

CDK1/Cks2 in complex with AZD5438. Determined by X-ray diffraction at 2.75 Å resolution. Released 5 Dec 2018.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,781
Mol. weight: 179.75 kDa
Ligands: FB8
Released: 5 Dec 2018

Explore 6GU7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GU7 contains 86 α-helices and 64 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	17-23	7	1
β-strand	29-36	8	1
α-helix	37-39	3
β-strand	40-41	2	2
α-helix	48-56	9
β-strand	63	1	3
β-strand	66-72	7	1
β-strand	75-81	7	1
β-strand	85-86	2	3
α-helix	87-92	6
α-helix	95	1
α-helix	102-121	20
α-helix	131-133	3
β-strand	134-136	3	3
β-strand	142-144	3	3
α-helix	149-152	4
α-helix	167-169	3
α-helix	172-175	4
β-strand	180-181	2	4
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	244-245	2
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-282	5
α-helix	285-287	3

Chains B and H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	5
α-helix	9-11	3
β-strand	12-13	2	5
β-strand	17-23	7	5
α-helix	24-25	2
α-helix	29-31	3
α-helix	40-45	6
β-strand	55-58	4	5
β-strand	66-72	7	5
α-helix	73-74	2

Chain C: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	6
β-strand	17-23	7	6
β-strand	29-36	8	6
α-helix	37-39	3
β-strand	40-41	2	7
α-helix	47-56	10
β-strand	63	1	8
β-strand	66-72	7	6
β-strand	75-81	7	6
β-strand	85-86	2	8
α-helix	87-92	6
α-helix	95	1
α-helix	102-121	20
α-helix	131-133	3
β-strand	134-136	3	8
β-strand	142-144	3	8
α-helix	149-152	4
α-helix	165-168	4
α-helix	172-175	4
β-strand	180-181	2	9
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	244-246	3
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-282	5
α-helix	285-287	3

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	10
α-helix	9-11	3
β-strand	12-13	2	10
β-strand	17-23	7	10
α-helix	29-31	3
α-helix	40-45	6
β-strand	55-58	4	10
β-strand	66-72	7	10
α-helix	73-74	2

Chain E: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	11
β-strand	17-23	7	11
β-strand	29-36	8	11
α-helix	37-39	3
β-strand	40-41	2	4
α-helix	47-56	10
β-strand	63	1	12
β-strand	66-71	6	11
β-strand	75-81	7	11
β-strand	85-86	2	12
α-helix	87-92	6
α-helix	95	1
α-helix	102-121	20
α-helix	131-133	3
β-strand	134-136	3	12
β-strand	142-144	3	12
α-helix	149-153	5
α-helix	167-169	3
α-helix	172-175	4
β-strand	180-181	2	2
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	244-245	2
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-282	5
α-helix	285-287	3

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	13
α-helix	9-11	3
β-strand	12-13	2	13
β-strand	17-23	7	13
α-helix	24-25	2
α-helix	29-31	3
α-helix	37-39	3
α-helix	40-45	6
β-strand	55-58	4	13
β-strand	66-72	7	13

Chain G: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	14
β-strand	17-23	7	14
β-strand	29-36	8	14
α-helix	37-39	3
β-strand	40-41	2	9
α-helix	47-56	10
β-strand	63	1	15
β-strand	66-72	7	14
β-strand	75-81	7	14
β-strand	85-86	2	15
α-helix	87-92	6
α-helix	95	1
α-helix	102-121	20
α-helix	131-133	3
β-strand	134-136	3	15
β-strand	142-144	3	15
α-helix	149-152	4
α-helix	167-169	3
α-helix	172-175	4
β-strand	180-181	2	7
α-helix	184-199	16
α-helix	209-220	12
α-helix	231-233	3
α-helix	258-267	10
α-helix	276-277	2
α-helix	278-282	5
α-helix	285-287	3

Molecules and chains

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

Sequence of entity 1 (A, C, E, G), FASTA

>6GU7_1 Cyclin-dependent kinase 1 (chains A, C, E, G)
GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLL
KELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQG
IVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVL
LGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQ
DYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIK
KM

Sequence of entity 2 (B, D, F, H), FASTA

>6GU7_2 Cyclin-dependent kinases regulatory subunit 2 (chains B, D, F, H)
GPLGSMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWV
HYMIHEPEPHILLFRRPLPKDQQK

Ligands and cofactors

ID	Name	Formula	Copies
FB8	4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin…	C18 H21 N5 O2 S	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
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
9SKQ 3.4 Å, Cryo-EM structure of CAK-CDK1-cyclin B1

Browse structure collections

About this viewer

MolViewer shows 6GU7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.