4PDS: Rad53 kinase domain and SCD2

Crystal structure of Rad53 kinase domain and SCD2 in complex with AMPPNP. Determined by X-ray diffraction at 2.9 Å resolution. Released 28 May 2014.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,614
Mol. weight: 77.87 kDa
Ligands: ANP
Released: 28 May 2014

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

Secondary structure: helices and β-sheets

4PDS contains 32 α-helices and 23 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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	193-196	4
β-strand	197-200	4	1
β-strand	212-217	6	1
β-strand	223-228	6	1
α-helix	244-250	7
β-strand	256	1	2
α-helix	257-258	2
β-strand	259-262	4	1
β-strand	270-274	5	1
β-strand	280	1	2
α-helix	281-288	8
α-helix	291-292	2
α-helix	293-312	20
β-strand	316	1	3
β-strand	325-329	5	2
β-strand	334-337	4	2
β-strand	344	1	3
α-helix	364-366	3
α-helix	386-403	18
α-helix	415-421	7
α-helix	427-432	6
α-helix	437-446	10
α-helix	451-453	3
α-helix	455-456	2
α-helix	457-461	5
α-helix	464-467	4
β-strand	477-478	2	4
α-helix	484-489	6

Chain B: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	193-196	4
β-strand	197-199	3	4
β-strand	211-217	7	4
β-strand	223-228	6	4
α-helix	244-250	7
β-strand	256	1	5
α-helix	257-258	2
β-strand	259-262	4	4
β-strand	270-274	5	4
β-strand	280	1	5
α-helix	281-288	8
α-helix	291-292	2
α-helix	293-312	20
β-strand	316	1	6
β-strand	325-329	5	5
β-strand	334-337	4	5
β-strand	344	1	6
α-helix	359-361	3
α-helix	364-366	3
α-helix	386-403	18
α-helix	415-421	7
α-helix	427-432	6
α-helix	437-446	10
α-helix	455-456	2
α-helix	457-461	5
α-helix	464-467	4
α-helix	484-493	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase RAD53	A, B	protein	347	Saccharomyces cerevisiae	P22216 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4PDS_1 Serine/threonine-protein kinase RAD53 (chains A, B)
GAMATSKIASPGLTSSTASSMVANKTGIFKDFSIIDEVVGQGAFATVKKAIERTTGKTFS
VKIISKRKVIGNMDGVTRELEVLQKLNHPRIVRLKGFYEDTESYYMVMEFVSGGDLMDFV
AAHGAVGEDAGREISRQILTAIKYIHSMGISHRDLKPDNILIEQDDPVLVKITAFGLAKV
QGNGSFMKTFCGTLAYVAPEVIRGKDTSVSPDEYEERNEYSSLVDMWSMGCLVYVILTGH
LPFSGSTQDQLYKQIGRGSYHEGPLKDFRISEEARDFIDSLLQVDPNNRSTAAKALNHPW
IKMSPLGSQSYGDFSQISLSQSLSQQKLLENMDDAQYEFVKAQRKLQ

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Structural basis of Rad53 kinase activation by dimerization and activation segment exchange. Wybenga-Groot, L.E., Ho, C.S., Sweeney, F.D. et al. Cell Signal (2014) 26:1825-1836. DOI 10.1016/j.cellsig.2014.05.004 · PubMed

Other PDB entries of the same protein (UniProt P22216 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1G6G 1.6 Å, X-ray structure of the N-terminal fha domain from S. Cerevisiae RAD53P in complex with a…
5T2S 2.4 Å, Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4…
4PDP 2.59 Å, Crystal structure of Rad53 kinase domain and SCD2
6C4U 2.6 Å, Engineered FHA with Myc-pTBD peptide
5T2F 2.66 Å, Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4
5XZW 2.8 Å, Crystal structure of Rad53 1-466
2YGV 2.94 Å, Conserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the…
5XZV 3.1 Å, Crystal structure of Rad53 1-466 in complex with AMP-PNP
1DMZ A refined NMR structure of a new phophopeptide-binding domain containing the FHA2 of RAD53
1FHQ Refined solution structure of the FHA2 domain of RAD53
1FHR Solution structure of the FHA2 domain of RAD53 complexed with a phosphotyrosyl peptide
1G3G NMR structure of the FHA1 domain of yeast RAD53

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