Minimal construct of Cdc7-Dbf4 bound to XL413. Determined by X-ray diffraction at 1.44 Å resolution. Released 27 May 2020.
Explore 6YA6 in 3D Show helices and sheets RCSB PDB PDBe
6YA6 contains 27 α-helices and 19 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 39-50 | 12 | |
| 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 | 98-106 | 9 | |
| α-helix | 107-111 | 5 | |
| 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 | |
| β-strand | 358-359 | 2 | 5 |
| α-helix | 361-364 | 4 | |
| α-helix | 367-369 | 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 | 6 |
| α-helix | 454-457 | 4 | |
| α-helix | 458-466 | 9 | |
| α-helix | 540-549 | 10 | |
| α-helix | 558-559 | 2 | |
| α-helix | 560-563 | 4 | |
| α-helix | 567-569 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 208-210 | 3 | |
| β-strand | 213-214 | 2 | 5 |
| α-helix | 215-216 | 2 | |
| β-strand | 219-224 | 6 | 6 |
| β-strand | 232-235 | 4 | 6 |
| α-helix | 247 | 1 | |
| β-strand | 294-296 | 3 | 7 |
| β-strand | 301-303 | 3 | 7 |
| α-helix | 306-309 | 4 | |
| α-helix | 313-319 | 7 | |
| α-helix | 325-331 | 7 | |
| β-strand | 338 | 1 | 2 |
| α-helix | 341-345 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell… | A | protein | 359 | Homo sapiens | O00311 (AlphaFold model) |
| Protein DBF4 homolog A | B | protein | 144 | Homo sapiens | Q9UBU7 (AlphaFold model) |
>6YA6_1 Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase (chains A) MLAGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPT SHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVR EYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQ SEAQQERCSQNKPASLTCDCYATDKVCSICLSRRQQVAPRAGTPGFRAPEVLTKCPNQTT AIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEV PAQDLRKLCERLRGAGAGGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDMSL
>6YA6_2 Protein DBF4 homolog A (chains B) GPGTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDVDKPSSMQKQTQ VKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQV VDDIVSKLVFDFVEYEKDTPKKKR
| ID | Name | Formula | Copies |
|---|---|---|---|
| 0SX | 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one | C14 H12 Cl N3 O2 | 1 |
| ZN | Zinc ion | Zn | 2 |
| BO3 | Boric acid | B H3 O3 | 1 |
Water and common crystallization additives (PEG, CL, IMD) are not listed.
Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase. Dick, S.D., Federico, S., Hughes, S.M. et al. Structure (2020) 28:954-962.e4. DOI 10.1016/j.str.2020.05.010 · PubMed
Other PDB entries of the same protein (UniProt O00311 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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