SAXSdb — 6mf6

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

Cell cycle serine/threonine-protein kinase CDC5/MSD2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DDK kinase regulatory subunit DBF4 × 1 （P32325）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DDK kinase regulatory subunit DBF4 × 1 （P32325）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDC5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–290； UniProt 418–705 Author chain B； PDBConstruct 3–290； UniProt 418–705

DDK kinase regulatory subunit DBF4

Saccharomyces cerevisiae

UniProt P32325

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cell cycle serine/threonine-protein kinase CDC5/MSD2 × 1 （P32562）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cell cycle serine/threonine-protein kinase CDC5/MSD2 × 1 （P32562）	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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–21； UniProt 76–96 Author chain D； PDBConstruct 1–21； UniProt 76–96

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	6mf6
Deposition date deposition_date	2018-09-09
Structure title title	Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region.
Keywords keywords	Mitosis, Dbf4, Polo-like kinases, CELL CYCLE, Transferase; CELL CYCLE, Transferase
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.

6mf6__assembly_1__model_1

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

Download this curve (.dat)

6mf6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mf6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.83 Å
Rg (electron density)	18.70 Å
Total Rg	19.71 Å
Atom count	3591
Residues	252
Excluded volume	32807 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mf6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6mf6__assembly_2__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Cell cycle serine/threonine-protein kinase CDC5/MSD2
Molecular weight formula_weight	33463.2 kDa
EC 编号 ec_number	2.7.11.21
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7178

GALSPGGTKQKYKEVVDIEAQRRLNDLAREARIRRAQQAVLRKELIATSTNVIKSEISLRILASECHLTLNGIVEAEAQYKMGGLPKSRLPKIKHPMIVTKWVDYSNKHGFSYQLSTEDIGVLFNNGTTVLRLADAEEFWYISYDDREGWVASHYLLSEKPRELSRHLEVVDFFAKYMKANLSRVSTFGREEYHKDDVFLRRYTRYKPFVMFELSDGTFQFNFKDHHKMAISDGGKLVTYISPSHESTTYPLVEVLKYGEIPGYPESNFREKLTLIKEGLKQKSTIVTVD

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	DDK kinase regulatory subunit DBF4
Molecular weight formula_weight	2246.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RARIERARSIEGAVQVSKGTG

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

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Unit-cell length a length_a	135.054 Å
Unit-cell length b length_b	135.054 Å
Unit-cell length c length_c	75.163 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	44.207 Å
R factor r_factor	0.2454
R_work r_work	0.2433
R_free r_free	0.2830

Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region.

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

Cell cycle serine/threonine-protein kinase CDC5/MSD2

State in the Current Structure

Other States of the Same Protein in the Database

DDK kinase regulatory subunit DBF4

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

6mf6__assembly_1__model_1

6mf6__assembly_1__model_1 | I(q)

6mf6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region.

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

Cell cycle serine/threonine-protein kinase CDC5/MSD2

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

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

6mf6__assembly_1__model_1

6mf6__assembly_1__model_1 | I(q)

6mf6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)