SAXSdb — 5t2s

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP × 1 GLYCEROL × 9 water × 2	Consistent with protein count
3	Insufficient information	Heteromer	Protein 4	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP × 2 GLYCEROL × 11 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD53_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 124–264； UniProt 22–162 Author chain C； PDBConstruct 124–264； UniProt 22–162

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53

Saccharomyces cerevisiae

UniProt P32325

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP × 1 GLYCEROL × 9 water × 2	Consistent with protein count
3	Insufficient information	Heteromer	Protein 4	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP × 2 GLYCEROL × 11 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DBF4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–119； UniProt 105–220 Author chain C； PDBConstruct 4–119； UniProt 105–220

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5t2s
Deposition date deposition_date	2016-08-24
Structure title title	Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.
Keywords keywords	FHA; BRCT; phosphopeptide; protein chimera, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5t2s__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5t2s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5t2s__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.60 Å
Rg (electron density)	23.77 Å
Total Rg	24.52 Å
Atom count	2026
Residues	255
Excluded volume	35974 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5t2s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5t2s__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5t2s__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53
Molecular weight formula_weight	30571.0 kDa
EC 编号 ec_number	2.7.12.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4285

SHMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHVDGSKFSQEQIGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQNKVDR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
Molecular weight formula_weight	1347.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

DGESTDEDDVVS

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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Unit-cell length a length_a	64.520 Å
Unit-cell length b length_b	87.260 Å
Unit-cell length c length_c	66.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	39.674 Å
R factor r_factor	0.2083
R_work r_work	0.2071
R_free r_free	0.2285

Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.

1. Protein Identity and Related Structures Protein Identity & Related Structures

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53

State in the Current Structure

Other States of the Same Protein in the Database

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5t2s__assembly_1__model_1

5t2s__assembly_1__model_1 | I(q)

5t2s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.

1. Protein Identity and Related Structures Protein Identity & Related Structures

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5t2s__assembly_1__model_1

5t2s__assembly_1__model_1 | I(q)

5t2s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)