1UNH: Cyclin-dependent kinase 5

Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Determined by X-ray diffraction at 2.35 Å resolution. Released 10 Nov 2004.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 7,086
Mol. weight: 113.65 kDa
Ligands: IXM
Released: 10 Nov 2004

Explore 1UNH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1UNH contains 45 α-helices and 22 β-strands across 4 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	17-23	7	1
β-strand	29-36	8	1
α-helix	44-55	12
β-strand	63	1	2
α-helix	64-65	2
β-strand	66-72	7	1
β-strand	75-81	7	1
β-strand	85-86	2	2
α-helix	87-93	7
α-helix	100-119	20
β-strand	122-123	2	3
α-helix	129-131	3
β-strand	132-134	3	2
β-strand	140-142	3	2
β-strand	149-150	2	3
α-helix	165-167	3
α-helix	170-173	4
α-helix	182-196	15
α-helix	208-219	12
α-helix	221-223	3
α-helix	228-232	5
α-helix	248-250	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-281	5

Chain B: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	4
β-strand	17-22	6	4
β-strand	29-36	8	4
α-helix	44-55	12
β-strand	63	1	5
β-strand	66-72	7	4
β-strand	75-81	7	4
β-strand	85-86	2	5
α-helix	87-93	7
α-helix	100-119	20
β-strand	122-123	2	6
α-helix	129-131	3
β-strand	132-134	3	5
β-strand	140-142	3	5
β-strand	149-150	2	6
α-helix	165-167	3
α-helix	170-173	4
α-helix	182-196	15
α-helix	208-219	12
α-helix	221-223	3
α-helix	228-232	5
α-helix	248-250	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-281	5

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	148-162	15
α-helix	172-185	14
α-helix	198-211	14
α-helix	219-237	19
α-helix	246-248	3
α-helix	254-277	24
α-helix	279-290	12

Chain E: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	148-162	15
α-helix	172-184	13
α-helix	198-211	14
α-helix	219-237	19
α-helix	246-248	3
α-helix	254-277	24
α-helix	279-290	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 5	A, B	protein	292	HOMO SAPIENS	Q00535 (AlphaFold model)
Cyclin-dependent kinase 5 activator 1	D, E	protein	208	HOMO SAPIENS	Q15078 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1UNH_1 CYCLIN-DEPENDENT KINASE 5 (chains A, B)
MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKH
KNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSR
NVLHRDLKPQNLLINRNGELKLANFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYS
TSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYKPYP
MYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP

Sequence of entity 2 (D, E), FASTA

>1UNH_2 CYCLIN-DEPENDENT KINASE 5 ACTIVATOR 1 (chains D, E)
QPPPAQPPAPPASQLSGSQTGGSSSVKKAPHPAVTSAGTPKRVIVQASTSELLRCLGEFL
CRRCYRLKHLSPTDPVLWLRSVDRSLLLQGWQDQGFITPANVVFLYMLCRDVISSEVGSD
HELQAVLLTCLYLSYSYMGNEISYPLKPFLVESCKEAFWDRCLSVINLMSSKMLQINADP
HYFTQVFSDLKNESGQEDKKRLLLGLDR

Ligands and cofactors

ID	Name	Formula	Copies
IXM	(z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-dione-3-oxime	C16 H11 N3 O2	2

Primary citation

Mechanism of Cdk5/P25 Binding by Cdk Inhibitors. Mapelli, M., Massimilinao, L., Crovace, C. et al. J Med Chem (2005) 48:671. DOI 10.1021/JM049323M · PubMed

Other PDB entries of the same protein (UniProt Q00535 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4AU8 1.9 Å, Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode…
3O0G 1.95 Å, Crystal Structure of Cdk5:p25 in complex with an ATP analogue
7VDP 2.09 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
9Q3N 2.1 Å, Crystal structure of human CDK5-cyclinB1 complex
1UNL 2.2 Å, Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and…
1UNG 2.3 Å, Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and…
9Q3O 2.5 Å, Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP
7VDR 2.55 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13
1H4L 2.65 Å, Structure and regulation of the CDK5-p25(nck5a) complex
7VDQ 2.91 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7
7VDS 3.05 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24

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