SAXSdb — 2zke

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

E3 ubiquitin-protein ligase UHRF1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(DCPDTPDAPDCPDCPDGPDGPDAPDTPDTPDGPDC)-3') ; × 1 ;DNA (5'-D(DGPDCPDAPDAPDTPDCP(5CM)PDGPDGPDTPDAPDG)-3') ; × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UHRF1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 404–613

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	2zke
Deposition date deposition_date	2008-03-19
Structure title title	Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Keywords keywords	;Protein-DNA interaction, Cell cycle, Developmental protein, DNA damage, DNA repair, DNA-binding, Ligase, Metal-binding, Nucleus, Phosphoprotein, Transcription, Transcription regulation, Ubl conjugation pathway, Zinc-finger ;; LIGASE
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.

2zke__assembly_1__model_1

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

Download this curve (.dat)

2zke__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zke__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.87 Å
Rg (electron density)	17.84 Å
Total Rg	18.77 Å
Atom count	2134
Residues	233
Excluded volume	35771 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zke__assembly_1__model_1`	trimeric （3）	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	E3 ubiquitin-protein ligase UHRF1
Molecular weight formula_weight	23407.1 kDa
EC 编号 ec_number	6.3.2.-
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	2153

SGMACVGRTTECTIVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTRQLGLTMQYPE

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DCPDTPDAPDCPDCPDGPDGPDAPDTPDTPDGPDC)-3') ;
Molecular weight formula_weight	3638.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CTACCGGATTGC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(DGPDCPDAPDAPDTPDCP(5CM)PDGPDGPDTPDAPDG)-3') ;
Molecular weight formula_weight	3701.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GCAATCCGGTAG

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2zkea_
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

CATH v4.4 (1 domains)

Domain ID domain_id	2zkeA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

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Unit-cell length a length_a	59.081 Å
Unit-cell length b length_b	59.081 Å
Unit-cell length c length_c	193.971 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	43.620 Å
R factor r_factor	0.2211
R_work r_work	0.2186
R_free r_free	0.2746

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA

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

E3 ubiquitin-protein ligase UHRF1

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

2zke__assembly_1__model_1

2zke__assembly_1__model_1 | I(q)

2zke__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 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA

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

E3 ubiquitin-protein ligase UHRF1

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

2zke__assembly_1__model_1

2zke__assembly_1__model_1 | I(q)

2zke__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 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)