6P8E: CDK4

Crystal structure of CDK4 in complex with CyclinD1 and P27. Determined by X-ray diffraction at 2.3 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,709
Mol. weight: 71.21 kDa
Ligands: MG
Released: 25 Dec 2019

Explore 6P8E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P8E contains 35 α-helices and 13 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, 0 β-strands

Element	Residues	Length
α-helix	20-34	15
α-helix	44-47	4
α-helix	54-70	17
α-helix	77-89	13
α-helix	96-98	3
α-helix	99-114	16
α-helix	118-120	3
α-helix	121-127	7
α-helix	134-147	14
α-helix	157-166	10
α-helix	172-190	19
α-helix	194-197	4
α-helix	200-211	12
α-helix	214-216	3
α-helix	226-237	12
α-helix	241-264	24

Chain B: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	21-24	4	1
β-strand	31-39	9	1
β-strand	42	1	2
β-strand	45	1	2
α-helix	48-63	16
β-strand	68	1	3
α-helix	69-70	2
β-strand	71-77	7	1
β-strand	84-92	9	1
β-strand	96	1	3
α-helix	97-102	6
α-helix	111-130	20
α-helix	140-142	3
β-strand	143-145	3	3
β-strand	151-153	3	3
α-helix	180-183	4
α-helix	191-206	16
α-helix	216-227	12
α-helix	229-231	3
α-helix	232-234	3
α-helix	236	1
α-helix	243-245	3
α-helix	250-253	4
α-helix	254-256	3
α-helix	263-272	10
α-helix	281-282	2
α-helix	283-287	5
α-helix	290-292	3

Chain C: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-60	23
β-strand	62-63	2	4
β-strand	68-69	2	4
β-strand	77-78	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G1/S-specific cyclin-D1	A	protein	249	Homo sapiens	P24385 (AlphaFold model)
Cyclin-dependent kinase 4	B	protein	302	Homo sapiens	P11802 (AlphaFold model)
Cyclin-dependent kinase inhibitor 1B	C	protein	72	Homo sapiens	P46527 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6P8E_1 G1/S-specific cyclin-D1 (chains A)
DANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVF
PLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELL
QMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISN
PPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEALLESS
LRQAQQNMD

Sequence of entity 2 (B), FASTA

>6P8E_2 Cyclin-dependent kinase 4 (chains B)
GEFATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGEEGLPISTVREVALLR
RLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLM
RQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYR
APEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRD
VSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYLHKDEGN
PE

Sequence of entity 3 (C), FASTA

>6P8E_3 Cyclin-dependent kinase inhibitor 1B (chains C)
GEFKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEK
GSLPEFYYRPPR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

p27 allosterically activates cyclin-dependent kinase 4 and antagonizes palbociclib inhibition. Guiley, K.Z., Stevenson, J.W., Lou, K. et al. Science (2019) 366. DOI 10.1126/science.aaw2106 · PubMed

Other PDB entries of the same protein (UniProt P24385 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CSK 2.25 Å, Crystal structure of CDK4 cyclin D1 in complex with atirmociclib
2W96 2.3 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
2W9Z 2.45 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
5VZU 2.7 Å, Crystal structure of the Skp1-FBXO31-cyclin D1 complex
2W99 2.8 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8G 2.8 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
2W9F 2.85 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8F 2.89 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
6P8H 3.19 Å, Crystal structure of CDK4 in complex with CyclinD1 and P21
9IVD 3.55 Å, Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1

Browse structure collections

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