4F9B: Human CDC7 kinase

Human CDC7 kinase in complex with DBF4 and PHA767491. Determined by X-ray diffraction at 2.5 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,669
Mol. weight: 115.67 kDa
Ligands: ZN, 0SY
Released: 31 Oct 2012

Explore 4F9B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F9B contains 43 α-helices and 35 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: 19 helices, 12 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	117	1	3
β-strand	122-126	5	1
β-strand	129-135	7	1
α-helix	142-145	4
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	560-564	5
α-helix	567-569	3

Chain B: 4 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
β-strand	295-296	2	6
β-strand	301-302	2	6
α-helix	306-311	6
α-helix	313-320	8
α-helix	325-331	7
β-strand	338	1	2

Chain C: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-50	11
α-helix	52-56	5
β-strand	58-66	9	7
β-strand	70-78	9	7
β-strand	79	1	8
β-strand	84-92	9	7
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
α-helix	197-199	3
β-strand	201-202	2	10
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	433-442	10
β-strand	445-449	5	11
α-helix	458-465	8
α-helix	540-549	10
α-helix	560-564	5
α-helix	567-569	3

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	219-224	6	11
β-strand	232-235	4	11
β-strand	295	1	12
β-strand	302	1	12
α-helix	306-311	6
α-helix	313-320	8
α-helix	325-331	7
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

>4F9B_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

>4F9B_2 Protein DBF4 homolog A (chains B, D)
GPGTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDVDKPSSMQKQTQ
VKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQV
VDDIVSKLVFDFVEYEKDTPKKKR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
0SY	2-(pyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one	C12 H11 N3 O	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
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
4F99 2.33 Å, Human CDC7 kinase in complex with DBF4 and nucleotide

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