4F99: Human CDC7 kinase

Human CDC7 kinase in complex with DBF4 and nucleotide. Determined by X-ray diffraction at 2.33 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,314
Mol. weight: 58.07 kDa
Ligands: ADP, MG, ZN
Released: 31 Oct 2012

Explore 4F99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F99 contains 26 α-helices and 17 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	42-50	9
α-helix	54-57	4
β-strand	59-66	8	1
β-strand	70-78	9	1
β-strand	79	1	2
β-strand	84-92	9	1
α-helix	98-110	13
β-strand	117	1	3
β-strand	122-126	5	1
β-strand	129-135	7	1
α-helix	142-146	5
α-helix	151-170	20
β-strand	173-174	2	4
α-helix	180-182	3
β-strand	183-186	4	3
β-strand	191-194	4	3
β-strand	201-202	2	4
α-helix	209-213	5
α-helix	215-216	2
α-helix	377-379	3
α-helix	382-385	4
α-helix	394-409	16
α-helix	420-431	12
α-helix	433-441	9
β-strand	445-449	5	5
α-helix	454-457	4
α-helix	458-465	8
α-helix	540-549	10
α-helix	558-559	2
α-helix	560-564	5
α-helix	567-569	3

Chain B: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	215-216	2
β-strand	219-224	6	5
β-strand	232-235	4	5
α-helix	247	1
β-strand	295-296	2	6
β-strand	301-302	2	6
α-helix	306-310	5
α-helix	313-319	7
α-helix	322-324	3
α-helix	325-331	7
β-strand	338	1	2
α-helix	339-341	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division cycle 7-related protein kinase	A	protein	361	Homo sapiens	O00311 (AlphaFold model)
Protein DBF4 homolog A	B	protein	144	Homo sapiens	Q9UBU7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4F99_1 Cell division cycle 7-related protein kinase (chains A)
MLAGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPT
SHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVR
EYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQ
SEAQQERCSQNKCSICLSRRQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSL
LSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRG
MDSSTPKLTSDIQGHATNLEGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDMS
L

Sequence of entity 2 (B), FASTA

>4F99_2 Protein DBF4 homolog A (chains B)
GPGTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDVDKPSSMQKQTQ
VKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQV
VDDIVSKLVFDFVEYEKDTPKKKR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Primary citation

Crystal structure of human CDC7 kinase in complex with its activator DBF4. Hughes, S., Elustondo, F., Di Fonzo, A. et al. Nat Struct Mol Biol (2012) 19:1101-1107. DOI 10.1038/nsmb.2404 · PubMed

Other PDB entries of the same protein (UniProt O00311 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YA6 1.44 Å, Minimal construct of Cdc7-Dbf4 bound to XL413
6YA7 1.67 Å, Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate
6YA8 1.79 Å, Cdc7-Dbf4 bound to ADP-BeF3
4F9C 2.08 Å, Human CDC7 kinase in complex with DBF4 and XL413
4F9A 2.17 Å, Human CDC7 kinase in complex with DBF4 and nucleotide
5UWR 2.24 Å, Crystal Structure of CDC7 NES Peptide (extended) in complex with CRM1-Ran-RanBP1
5UWQ 2.28 Å, Crystal Structure of CDC7 NES Peptide in complex with CRM1-Ran-RanBP1
4F9B 2.5 Å, Human CDC7 kinase in complex with DBF4 and PHA767491

Browse structure collections

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