5XZV: Rad53 1-466

Crystal structure of Rad53 1-466 in complex with AMP-PNP. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 5,444
Mol. weight: 106.03 kDa
Ligands: ANP
Released: 11 Oct 2017

Explore 5XZV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XZV contains 32 α-helices and 42 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: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	17-22	6
β-strand	32-38	7	1
β-strand	46-49	4	1
α-helix	52-57	6
β-strand	64-68	5	2
β-strand	88-93	6	2
α-helix	95-97	3
β-strand	99-104	6	2
β-strand	109-111	3	1
β-strand	114-115	2	1
β-strand	118	1	2
β-strand	122-124	3	2
β-strand	129-133	5	1
β-strand	140-147	8	1
α-helix	149-163	15
β-strand	197-206	10	3
β-strand	210-217	8	3
β-strand	223-230	8	3
α-helix	231-234	4
α-helix	238-248	11
β-strand	256	1	4
β-strand	259-264	6	3
β-strand	268-274	7	3
β-strand	280	1	4
α-helix	281-288	8
α-helix	293-312	20
β-strand	316	1	5
α-helix	322-324	3
β-strand	325-329	5	4
β-strand	334-337	4	4
β-strand	343	1	5
α-helix	364-366	3
α-helix	384-402	19
α-helix	413-422	10
α-helix	434-436	3
α-helix	437-443	7
α-helix	457-462	6

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	6
α-helix	44-45	2
β-strand	46-48	3	6
α-helix	52-56	5
β-strand	64-69	6	7
β-strand	76-77	2	7
β-strand	89-93	5	7
β-strand	99-103	5	7
β-strand	110-111	2	6
β-strand	114-115	2	6
β-strand	121-124	4	7
β-strand	129-131	3	6
β-strand	143-147	5	6
α-helix	149-156	8
α-helix	192-195	4
β-strand	197-199	3	8
β-strand	210-217	8	8
β-strand	222-229	8	8
α-helix	240-250	11
β-strand	256	1	9
β-strand	259-264	6	8
β-strand	269-274	6	8
β-strand	280	1	9
α-helix	281-288	8
α-helix	293-312	20
α-helix	322-324	3
β-strand	325-329	5	9
β-strand	334-337	4	9
α-helix	359-361	3
α-helix	364-367	4
α-helix	384-403	20
α-helix	413-421	9
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase RAD53	A, B	protein	471	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22216 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5XZV_1 Serine/threonine-protein kinase RAD53 (chains A, B)
MENITQPTQQSTQATQRFLIEKFSQEQIGENIVCRVICTTGQIPIRDLSADISQVLKEKR
SIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNS
NQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQNKVDRIRSNLKNTSKIASPGLTS
STASSMVANKTGIFKDFSIIDEVVGQGAFATVKKAIERTTGKTFAVKIISKRKVIGNMDG
VTRELEVLQKLNHPRIVRLKGFYEDTESYYMVMEFVSGGDLMDFVAAHGAVGEDAGREIS
RQILTAIKYIHSMGISHRDLKPDNILIEQDDPVLVKITDFGLAKVQGNGSFMKTFCGTLA
YVAPEVIRGKDTSVSPDEYEERNEYSSLVDMWSMGCLVYVILTGHLPFSGSTQDQLYKQI
GRGSYHEGPLKDFRISEEARDFIDSLLQVDPNNRSTAAKALNHPWIVDSSN

Ligands and cofactors

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

Primary citation

Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation. Chen, E.S., Weng, J.H., Chen, Y.H. et al. Biochemistry (2017) 56:5112-5124. DOI 10.1021/acs.biochem.7b00689 · 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
4PDS 2.9 Å, Crystal structure of Rad53 kinase domain and SCD2 in complex with AMPPNP
2YGV 2.94 Å, Conserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the…
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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