4X9R: PLK-1 polo-box domain

PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide macrocycle 3B. Determined by X-ray diffraction at 1.4 Å resolution. Released 29 Jul 2015.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,114
Mol. weight: 28.25 kDa
Released: 29 Jul 2015

Explore 4X9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X9R contains 11 α-helices and 15 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 A: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	374-386	13
α-helix	389-391	3
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
β-strand	467	1	2
α-helix	470-472	3
α-helix	473-488	16
α-helix	491-492	2
α-helix	498-501	4
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	574-591	18

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase PLK1	A	protein	237	Homo sapiens	P53350 (AlphaFold model)
Phosphopeptide macrocycle 3B	B	protein	6	synthetic construct

Sequence of entity 1 (A), FASTA

>4X9R_1 Serine/threonine-protein kinase PLK1 (chains A)
GAHMDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQ
LCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYM
SEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPL
MAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS

Sequence of entity 2 (B), FASTA

>4X9R_2 Phosphopeptide macrocycle 3B (chains B)
XLHSTX

Primary citation

Neighbor-directed histidine N ( tau )-alkylation: A route to imidazolium-containing phosphopeptide macrocycles. Qian, W.J., Park, J.E., Grant, R. et al. Biopolymers (2015) 104:663-673. DOI 10.1002/bip.22698 · PubMed

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

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
9QMO 1.6 Å, PLK1 PBD apo protein at 1.6A

Browse structure collections

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