9Q3N: Human CDK5-cyclinB1 complex

Crystal structure of human CDK5-cyclinB1 complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 26 Aug 2026.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,766
Mol. weight: 69.72 kDa
Ligands: P4K
Released: 26 Aug 2026

Explore 9Q3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3N contains 34 α-helices and 12 β-strands across 2 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 B: 15 helices, 12 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	46-57	12
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	97-99	3
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
β-strand	153-154	2	3
α-helix	170-173	4
α-helix	182-195	14
α-helix	208-219	12
α-helix	221-223	3
α-helix	242-245	4
α-helix	248-250	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-280	4

Chain C: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	175-184	10
α-helix	199-216	18
α-helix	220-235	16
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	317-330	14
α-helix	334-336	3
α-helix	341-356	16
α-helix	363-367	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 5	B	protein	295	Homo sapiens	Q00535 (AlphaFold model)
G2/mitotic-specific cyclin-B1	C	protein	285	Homo sapiens	P14635 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9Q3N_1 Cyclin-dependent kinase 5 (chains B)
SNAMQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKE
LKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFC
HSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAK
LYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYK
PYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP

Sequence of entity 2 (C), FASTA

>9Q3N_2 G2/mitotic-specific cyclin-B1 (chains C)
SNAAVNDVDAEDGADPNLSSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDW
LVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGD
FAFVTDNTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLME
LTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVV
MVNQGLTKHMTVKNKYATSKHAKISTLPQLNSALVQDLAKAVAKV

Ligands and cofactors

ID	Name	Formula	Copies
P4K	polyethylene glycol	C30 H62 O15	5

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Crystal structure of human CDK5-cyclinB1 complex. Syed, A., Arvai, A.S., Chowdhury, D. et al. To be published.

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
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…
1UNH 2.35 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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