9Q3O: Human CDK5-cyclinB1 complex

Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Aug 2026.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,710
Mol. weight: 69.59 kDa
Ligands: P4K, ANP
Released: 26 Aug 2026

Explore 9Q3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3O contains 37 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: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
β-strand	16-23	8	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	100-118	19
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	158-160	3
α-helix	170-173	4
α-helix	182-195	14
α-helix	208-219	12
α-helix	221-223	3
α-helix	238-240	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	277-281	5

Chain C: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	175-184	10
α-helix	199-215	17
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	301-310	10
α-helix	317-329	13
α-helix	330-332	3
α-helix	334-336	3
α-helix	341-355	15
α-helix	363-372	10
α-helix	377-391	15
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

>9Q3O_1 Cyclin-dependent kinase 5 (chains B)
SNAMQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKE
LKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFC
HSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAK
LYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYK
PYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP

Sequence of entity 2 (C), FASTA

>9Q3O_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	4
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

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

Primary citation

Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP. 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
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…
1UNH 2.35 Å, Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and…
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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