SAXSdb — 2od8

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

Proliferating cell nuclear antigen

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA ligase I, mitochondrial precursor × 3 （P04819） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 1–258

DNA ligase I, mitochondrial precursor

OrganismNot specified

UniProt P04819

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Proliferating cell nuclear antigen × 3 （P15873） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNLI_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–22； UniProt 32–53

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	2od8
Deposition date deposition_date	2006-12-21
Structure title title	Structure of a peptide derived from Cdc9 bound to PCNA
Keywords keywords	homotrimer, PCNA-peptide complex, PCNA, PROTEIN BINDING; PROTEIN BINDING
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.

2od8__assembly_1__model_1

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

Download this curve (.dat)

2od8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2od8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.70 Å
Rg (electron density)	32.58 Å
Total Rg	33.39 Å
Atom count	6285
Residues	798
Excluded volume	113440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2od8__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	Proliferating cell nuclear antigen
Molecular weight formula_weight	28944.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2113

MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA ligase I, mitochondrial precursor
Molecular weight formula_weight	2456.9 kDa
EC 编号 ec_number	6.5.1.1
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AGKKPKQATLARFFTSMKNKPT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2od8a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d2od8a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

CATH v4.4 (1 domains)

Domain ID domain_id	2od8A00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	139.280 Å
Unit-cell length b length_b	139.280 Å
Unit-cell length c length_c	139.280 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.700 Å
R factor r_factor	0.2487
R_work r_work	0.2468
R_free r_free	0.2853

Structure of a peptide derived from Cdc9 bound to PCNA

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

Proliferating cell nuclear antigen

State in the Current Structure

Other States of the Same Protein in the Database

DNA ligase I, mitochondrial precursor

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

2od8__assembly_1__model_1

2od8__assembly_1__model_1 | I(q)

2od8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of a peptide derived from Cdc9 bound to PCNA

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

Proliferating cell nuclear antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA ligase I, mitochondrial precursor

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

2od8__assembly_1__model_1

2od8__assembly_1__model_1 | I(q)

2od8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)