SAXSdb — 2c56

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

URACIL DNA GLYCOSYLASE

HUMAN HERPESVIRUS 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_HHV11
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–244； UniProt 91–334

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	2c56
Deposition date deposition_date	2005-10-26
Structure title title	A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1
Keywords keywords	HYDROLASE, URACIL DNA GLYCOSYLASE, DNA REPAIR, DNA DAMAGE, GLYCOSIDASE; HYDROLASE
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.

2c56__assembly_1__model_1

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

Download this curve (.dat)

2c56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.36 Å
Rg (electron density)	17.07 Å
Total Rg	18.12 Å
Atom count	1820
Residues	228
Excluded volume	32339 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c56__assembly_1__model_1`	monomeric （1）	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	URACIL DNA GLYCOSYLASE
Molecular weight formula_weight	27341.4 kDa
EC 编号 ec_number	3.2.2.3
Mutation mutation	YES
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	2102

MDLTNGGVSPAATSAPLDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQNPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSNPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV

Source Source

Source organism organism	HUMAN HERPESVIRUS 1
NCBI taxonomy ID ncbi_taxonomy_id	10298
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	259

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2c56a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.18 — Uracil-DNA glycosylase-like
Superfamily Superfamily superfamily	c.18.1 — Uracil-DNA glycosylase-like
Family Family family	c.18.1.1 — Uracil-DNA glycosylase

CATH v4.4 (1 domains)

Domain ID domain_id	2c56A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	470 — Uracil-DNA Glycosylase, subunit E
Homologous superfamily homologous superfamily	10 — Uracil-DNA glycosylase-like domain

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Unit-cell length a length_a	42.040 Å
Unit-cell length b length_b	61.117 Å
Unit-cell length c length_c	43.392 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.590 Å
R factor r_factor	0.1510
R_work r_work	0.1510
R_free r_free	0.2120

A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1

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

URACIL DNA GLYCOSYLASE

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

2c56__assembly_1__model_1

2c56__assembly_1__model_1 | I(q)

2c56__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 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1

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

URACIL DNA GLYCOSYLASE

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

2c56__assembly_1__model_1

2c56__assembly_1__model_1 | I(q)

2c56__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 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)