3QBZ: DDK kinase regulatory subunit DBF4

Crystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4. Determined by X-ray diffraction at 2.69 Å resolution. Released 7 Dec 2011.

Method: X-ray diffraction
Resolution: 2.69 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 1,068
Mol. weight: 19.28 kDa
Released: 7 Dec 2011

Explore 3QBZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QBZ contains 6 α-helices and 4 β-strands across 1 chain. 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	106-118	13
α-helix	119-123	5
β-strand	125-128	4	1
α-helix	138-156	19
β-strand	161-163	3	1
β-strand	172-175	4	1
α-helix	182-184	3
α-helix	190-196	7
β-strand	200-203	4	1
α-helix	204-212	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDK kinase regulatory subunit DBF4	A	protein	160	Saccharomyces cerevisiae	P32325 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3QBZ_1 DDK kinase regulatory subunit DBF4 (chains A)
GSHMQQQQHLHEKKRARIERARSIEGAVQVSKGTGLKNVEPRVTPKELLEWQTNWKKIMK
RDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVEN
IYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHL

Primary citation

Saccharomyces cerevisiae Dbf4 has unique fold necessary for interaction with Rad53 kinase. Matthews, L.A., Jones, D.R., Prasad, A.A. et al. J Biol Chem (2012) 287:2378-2387. DOI 10.1074/jbc.M111.233973 · PubMed

Other PDB entries of the same protein (UniProt P32325 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3OQ4 2.4 Å, Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4
5T2S 2.4 Å, Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4…
5T2F 2.66 Å, Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4
3OQ0 2.7 Å, Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4
7V3V 2.9 Å, Cryo-EM structure of MCM double hexamer bound with DDK in State I
7PT6 3.2 Å, Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III
7P5Z 3.3 Å, Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase
6MF6 3.4 Å, Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4…
7PT7 3.8 Å, Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I

Browse structure collections

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