SAXSdb — 5nxq

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

DNA polymerase alpha-binding protein

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU × 2 GLYCEROL × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTF4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–479； UniProt 471–927 Author chain B； PDBConstruct 23–479； UniProt 471–927 Author chain C； PDBConstruct 23–479； UniProt 471–927

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	5nxq
Deposition date deposition_date	2017-05-10
Structure title title	Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP
Keywords keywords	DNA replication, adaptor protein, beta-propeller domain, replication; REPLICATION
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.

5nxq__assembly_1__model_1

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

Download this curve (.dat)

5nxq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nxq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.88 Å
Rg (electron density)	33.94 Å
Total Rg	34.57 Å
Atom count	9543
Residues	1177
Excluded volume	170440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nxq__assembly_1__model_1`	pentameric （5）	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	DNA polymerase alpha-binding protein
Molecular weight formula_weight	54534.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9931

MGSSHHHHHHSQDPENLYFQGSTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU
Molecular weight formula_weight	2309.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

MDIXIDDILXELDKETTAV

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

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Unit-cell length a length_a	88.679 Å
Unit-cell length b length_b	100.287 Å
Unit-cell length c length_c	219.749 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.413 Å
Low-resolution limit resolution_low	49.209 Å
R factor r_factor	0.1858
R_work r_work	0.1844
R_free r_free	0.2114

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP

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

DNA polymerase alpha-binding protein

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

5nxq__assembly_1__model_1

5nxq__assembly_1__model_1 | I(q)

5nxq__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 (2)

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP

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

DNA polymerase alpha-binding protein

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

5nxq__assembly_1__model_1

5nxq__assembly_1__model_1 | I(q)

5nxq__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 (2)