6MF5: Budding yeast Cdc5 polo-box domain

Crystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72 phosphopeptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 19 Feb 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 3,815
Mol. weight: 69.22 kDa
Released: 19 Feb 2020

Explore 6MF5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MF5 contains 16 α-helices and 32 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	437-450	14
β-strand	464-465	2	1
α-helix	471-492	22
α-helix	510-512	3
β-strand	514-520	7	2
β-strand	525-530	6	2
β-strand	535-538	4	2
β-strand	544-547	4	2
β-strand	553-560	8	2
β-strand	564-571	8	2
α-helix	580-596	17
β-strand	597	1	3
β-strand	615-620	6	1
β-strand	624-629	6	1
β-strand	634-638	5	1
β-strand	643-647	5	1
α-helix	648-650	3
β-strand	652-656	5	1
β-strand	662-666	5	1
α-helix	667-673	7
α-helix	684-698	15

Chain B: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	437-451	15
β-strand	464-465	2	4
α-helix	466-468	3
α-helix	471-496	26
α-helix	510-512	3
β-strand	514-519	6	5
α-helix	521-524	4
β-strand	526-530	5	5
β-strand	535-538	4	5
β-strand	544-547	4	5
β-strand	553-559	7	5
β-strand	565-571	7	5
α-helix	582-596	15
β-strand	597	1	6
α-helix	598-600	3
β-strand	615-620	6	4
β-strand	624-629	6	4
β-strand	634-638	5	4
β-strand	643-647	5	4
β-strand	652-656	5	4
β-strand	662-666	5	4
α-helix	667-673	7
α-helix	684-700	17

Chains C and D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	229-230	2	2
β-strand	233	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell cycle serine/threonine-protein kinase CDC5/MSD2	A, B	protein	290	Saccharomyces cerevisiae	P32562 (AlphaFold model)
Spc72	C, D	protein	11	Saccharomyces cerevisiae	P39723 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6MF5_1 Cell cycle serine/threonine-protein kinase CDC5/MSD2 (chains A, B)
GALSPGGTKQKYKEVVDIEAQRRLNDLAREARIRRAQQAVLRKELIATSTNVIKSEISLR
ILASECHLTLNGIVEAEAQYKMGGLPKSRLPKIKHPMIVTKWVDYSNKHGFSYQLSTEDI
GVLFNNGTTVLRLADAEEFWYISYDDREGWVASHYLLSEKPRELSRHLEVVDFFAKYMKA
NLSRVSTFGREEYHKDDVFLRRYTRYKPFVMFELSDGTFQFNFKDHHKMAISDGGKLVTY
ISPSHESTTYPLVEVLKYGEIPGYPESNFREKLTLIKEGLKQKSTIVTVD

Sequence of entity 2 (C, D), FASTA

>6MF5_2 Spc72 (chains C, D)
SLAQSSPAGSQ

Primary citation

Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division. Almawi, A.W., Langlois-Lemay, L., Boulton, S. et al. Sci Rep (2020) 10:3379-3379. DOI 10.1038/s41598-020-60344-4 · PubMed

Other PDB entries of the same protein (UniProt P32562 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MF4 1.8 Å, Crystal structure of the polo-box domain of Cdc5 from budding yeast.
6MF6 3.4 Å, Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4…

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