4EOP: Cyclin-dependent kinase 2

Thr 160 phosphorylated CDK2 Q131E - human cyclin A3 complex with the inhibitor RO3306. Determined by X-ray diffraction at 1.99 Å resolution. Released 6 Feb 2013.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,518
Mol. weight: 128.46 kDa
Ligands: MG, SGM, 1RO
Released: 6 Feb 2013

Explore 4EOP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EOP contains 76 α-helices and 24 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: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
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	66-70	5	1
β-strand	75-81	7	1
β-strand	85-86	2	2
α-helix	87-93	7
α-helix	101-120	20
β-strand	123-124	2	3
α-helix	130-132	3
β-strand	133-135	3	2
β-strand	141-143	3	2
β-strand	150-151	2	3
α-helix	166-168	3
α-helix	171-174	4
α-helix	183-198	16
α-helix	208-219	12
α-helix	230-232	3
α-helix	240-242	3
α-helix	244-247	4
α-helix	248-251	4
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-280	4
α-helix	284-286	3
α-helix	292-295	4

Chain B: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	179-192	14
α-helix	194-196	3
α-helix	199-202	4
α-helix	208-224	17
α-helix	229-245	17
α-helix	253-268	16
α-helix	272-274	3
α-helix	275-281	7
α-helix	288-301	14
α-helix	311-319	9
α-helix	327-342	16
α-helix	344-347	4
α-helix	352-368	17
α-helix	374-380	7
α-helix	384-400	17
α-helix	401-403	3
α-helix	408-412	5
α-helix	416-418	3
α-helix	421-423	3
α-helix	425-427	3

Chain C: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	4
β-strand	17-23	7	4
β-strand	29-36	8	4
β-strand	38	1	5
β-strand	43	1	5
α-helix	46-57	12
β-strand	63	1	6
α-helix	64-65	2
β-strand	66-70	5	4
β-strand	75-81	7	4
β-strand	85-86	2	6
α-helix	87-93	7
α-helix	101-120	20
β-strand	123-124	2	7
α-helix	130-132	3
β-strand	133-135	3	6
β-strand	141-143	3	6
β-strand	150-151	2	7
α-helix	166-168	3
α-helix	171-174	4
α-helix	183-198	16
α-helix	208-219	12
α-helix	230-232	3
α-helix	243-247	5
α-helix	248-250	3
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-281	5
α-helix	284-286	3
α-helix	292-294	3

Chain D: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	179-192	14
α-helix	199-202	4
α-helix	208-224	17
α-helix	229-245	17
α-helix	250-252	3
α-helix	253-268	16
α-helix	272-274	3
α-helix	275-280	6
α-helix	288-301	14
α-helix	311-318	8
α-helix	319-321	3
α-helix	327-342	16
α-helix	344-347	4
α-helix	352-367	16
α-helix	374-380	7
α-helix	388-400	13
α-helix	401-403	3
α-helix	408-412	5
α-helix	416-418	3
α-helix	421-423	3
α-helix	425-426	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 2	A, C	protein	300	Homo sapiens	P24941 (AlphaFold model)
Cyclin-A2	B, D	protein	258	Homo sapiens	P20248 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4EOP_1 Cyclin-dependent kinase 2 (chains A, C)
PGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKE
LNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAF
CHSHRVLHRDLKPENLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGC
KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYK
PSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLR

Sequence of entity 2 (B, D), FASTA

>4EOP_2 Cyclin-A2 (chains B, D)
VPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHL
AVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRM
EHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSV
IAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYK
NSKYHGVSLLNPPETLNL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
SGM	Monothioglycerol	C3 H8 O2 S	1
1RO	(5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(…	C18 H13 N3 O S2	2

Primary citation

An integrated chemical biology approach provides insight into Cdk2 functional redundancy and inhibitor sensitivity. Echalier, A., Cot, E., Camasses, A. et al. Chem Biol (2012) 19:1028-1040. DOI 10.1016/j.chembiol.2012.06.015 · PubMed

Other PDB entries of the same protein (UniProt P24941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q4G 0.98 Å, CDK2 in complex with FragLite37
6Q49 1.0 Å, CDK2 in complex with FragLite6
6Q4H 1.0 Å, CDK2 in complex with FragLite36
6Q48 1.03 Å, CDK2 in complex with FragLite7
6Q4J 1.05 Å, CDK2 in complex with FragLite34
6Q4E 1.06 Å, CDK2 in complex with FragLite33
6Q4K 1.06 Å, CDK2 in complex with FragLite38
6Q4D 1.07 Å, CDK2 in complex with FragLite31
6Q3B 1.11 Å, CDK2 in complex with FragLite2
6Q4I 1.11 Å, CDK2 in complex with FragLite35
6Q4B 1.12 Å, CDK2 in complex with FragLite13
6Q4A 1.13 Å, CDK2 in complex with FragLite14

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