4F9A: Human CDC7 kinase

Human CDC7 kinase in complex with DBF4 and nucleotide. Determined by X-ray diffraction at 2.17 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,643
Mol. weight: 116.15 kDa
Ligands: ADP, MG, ZN
Released: 31 Oct 2012

Explore 4F9A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F9A contains 49 α-helices and 36 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: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-50	11
α-helix	52-56	5
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	93	1
α-helix	98-110	13
β-strand	114	1	3
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	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	560-564	5
α-helix	567-569	3

Chain B: 6 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	306-309	4
α-helix	313-320	8
α-helix	325-331	7
α-helix	335-336	2
β-strand	338	1	2

Chain C: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	38-50	13
α-helix	52-56	5
β-strand	59-66	8	7
β-strand	70-78	9	7
β-strand	79	1	8
β-strand	84-92	9	7
α-helix	93	1
α-helix	98-110	13
β-strand	114	1	9
β-strand	117	1	9
β-strand	122-126	5	7
β-strand	129-135	7	7
α-helix	142-146	5
α-helix	151-170	20
β-strand	173-174	2	10
α-helix	180-182	3
β-strand	183-186	4	9
β-strand	191-194	4	9
β-strand	201-202	2	10
α-helix	209-212	4
α-helix	377-379	3
α-helix	382-385	4
α-helix	394-409	16
α-helix	420-431	12
α-helix	433-442	10
β-strand	445-449	5	11
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 D: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	215-216	2
β-strand	219-224	6	11
β-strand	232-235	4	11
β-strand	295-296	2	12
β-strand	301-302	2	12
α-helix	306-311	6
α-helix	313-319	7
α-helix	322-324	3
α-helix	325-331	7
α-helix	335-336	2
β-strand	338	1	8

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>4F9A_1 Cell division cycle 7-related protein kinase (chains A, C)
MLAGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPT
SHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVR
EYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQ
SEAQQERCSQNKCSICLSRRQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSL
LSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRG
MDSSTPKLTSDIQGHATNLEGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDMS
L

Sequence of entity 2 (B, D), FASTA

>4F9A_2 Protein DBF4 homolog A (chains B, D)
GPGTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDVDKPSSMQKQTQ
VKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQV
VDDIVSKLVFDFVEYEKDTPKKKR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

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
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
4F99 2.33 Å, Human CDC7 kinase in complex with DBF4 and nucleotide
4F9B 2.5 Å, Human CDC7 kinase in complex with DBF4 and PHA767491

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