SAXSdb — 4jgc

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

G/T mismatch-specific thymine DNA glycosylase

Homo sapiens

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	oligonucleotide × 1 oligonucleotide containing 5-carboxylcytosine × 1 4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TDG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–204； UniProt 111–308

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	4jgc
Deposition date deposition_date	2013-02-28
Structure title title	Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC)
Keywords keywords	;5-carboxylcytosine; thymine DNA glycosylase; DNA modification; DNA 5mC oxidation; epigenetic regulation, DNA demethylation, 5-carboxylcytosine, HYDROLASE-DNA complex ;; HYDROLASE/DNA
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.

4jgc__assembly_1__model_1

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

Download this curve (.dat)

4jgc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jgc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.70 Å
Rg (electron density)	25.45 Å
Total Rg	26.05 Å
Atom count	2668
Residues	251
Excluded volume	43954 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jgc__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 (5)

Entity 1 Entity 1 polymer

Description description	G/T mismatch-specific thymine DNA glycosylase
Molecular weight formula_weight	23027.6 kDa
EC 编号 ec_number	3.2.2.29
Mutation mutation	N140A
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	2698

GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGIAPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	oligonucleotide
Molecular weight formula_weight	8646.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CAGCTCTGTACGTGAGCAGTGGACAGCT

Entity 3 Entity 3 polymer

Description description	oligonucleotide containing 5-carboxylcytosine
Molecular weight formula_weight	8473.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AGCTGTCCACTGCTCAXGTACAGAGCTG

Entity 4 Entity 4 non-polymer

Description description	4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid
Molecular weight formula_weight	155.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4jgcA00
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	91.486 Å
Unit-cell length b length_b	53.555 Å
Unit-cell length c length_c	81.902 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.582 Å
Low-resolution limit resolution_low	45.560 Å
R factor r_factor	0.2324
R_work r_work	0.2298
R_free r_free	0.2833

Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC)

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

G/T mismatch-specific thymine 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

4jgc__assembly_1__model_1

4jgc__assembly_1__model_1 | I(q)

4jgc__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC)

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

G/T mismatch-specific thymine 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

4jgc__assembly_1__model_1

4jgc__assembly_1__model_1 | I(q)

4jgc__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)