9FJG: Two PLK1 PBD proteins

Two PLK1 PBD proteins bound to CENP-U(58-114) phosphorylated at Thr98. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Sept 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,110
Mol. weight: 67.49 kDa
Ligands: FLC
Released: 24 Sept 2025

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

Secondary structure: helices and β-sheets

9FJG contains 23 α-helices and 30 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: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	372-386	15
α-helix	397-400	4
β-strand	401	1	1
α-helix	403-405	3
β-strand	411-417	7	2
β-strand	422-427	6	2
β-strand	432-436	5	2
β-strand	441-444	4	2
β-strand	450-454	5	2
β-strand	460-464	5	2
α-helix	470-472	3
α-helix	473-489	17
β-strand	490	1	3
α-helix	491-492	2
α-helix	497-499	3
α-helix	507-509	3
β-strand	511-516	6	1
β-strand	520-525	6	1
β-strand	530-534	5	1
β-strand	540-544	5	1
β-strand	549-553	5	1
β-strand	559-563	5	1
α-helix	564-570	7
α-helix	574-592	19

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	372-386	15
α-helix	397-400	4
β-strand	401	1	4
α-helix	403-405	3
β-strand	411-417	7	5
β-strand	422-427	6	5
β-strand	432-436	5	5
β-strand	441-444	4	5
β-strand	450-454	5	5
β-strand	460-464	5	5
α-helix	473-489	17
α-helix	498-500	3
α-helix	503-505	3
α-helix	507-509	3
β-strand	511-516	6	4
β-strand	520-525	6	4
β-strand	530-534	5	4
β-strand	540-544	5	4
α-helix	545-547	3
β-strand	549-553	5	4
β-strand	559-563	5	4
α-helix	564-570	7
α-helix	574-592	19

Chain C: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	75-76	2	2
β-strand	79	1	3
α-helix	80-82	3
α-helix	84-93	10
β-strand	96	1	5
α-helix	98-100	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase PLK1	A, B	protein	261	Homo sapiens	P53350 (AlphaFold model)
Centromere protein U	C	protein	59	Homo sapiens	Q71F23 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9FJG_1 Serine/threonine-protein kinase PLK1 (chains A, B)
GSKGLENPLPERPREKEEPVVRETGEVVDCHLSDMLQQLHSVNASKPSERGLVRQEEAED
PACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESY
LTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAII
LHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRY
ARTMVDKLLSSRSASNRLKAS

Sequence of entity 2 (C), FASTA

>9FJG_2 Centromere protein U (chains C)
GSLGENEKDEETYETFDPPLHSTAIYADEEEFSKHCGLSLSSTPPGKEAKRSSDTSGNE

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	1

Water and common crystallization additives (PG4, PEG) are not listed.

Primary citation

Two PLK1 PBD proteins bound to CENP-U(58-114) phosphorylated at Thr98. Ren, L., Musacchio, A. To be published.

Other PDB entries of the same protein (UniProt P53350 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4X9R 1.4 Å, PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide…
3P34 1.4 Å, Polo-like kinase I Polo-box domain in complex with MQSpTPL phosphopeptide
3Q1I 1.4 Å, Polo-like kinase I Polo-box domain in complex with FMPPPMSpSM phosphopeptide from TCERG1
4X9V 1.43 Å, PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide…
4O6W 1.45 Å, Peptide-Based Inhibitors of Plk1 Polo-box Domain
6AX4 1.45 Å, Plk-1 polo-box domain in complex with histidine N(tau)-cyclized Macrocycle 5b.
3RQ7 1.55 Å, Polo-like kinase 1 Polo box domain in complex with a C6H5(CH2)8-derivatized peptide…
4DFW 1.55 Å, Oxime-based Post Solid-phase Peptide Diversification: Identification of High Affinity…
3FVH 1.58 Å, Polo-like kinase 1 Polo box domain in complex with Ac-LHSpTA-NH2 peptide
4LKL 1.58 Å, Crystal structure of Plk1 Polo-box domain in complex with PL-55
3P36 1.59 Å, Polo-like kinase I Polo-box domain in complex with DPPLHSpTA phosphopeptide from PBIP1
4RCP 1.6 Å, Crystal structure of Plk1 Polo-box domain in complex with PL-2

Browse structure collections

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