SAXSdb — 5ayr

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

Uracil-DNA glycosylase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Uncharacterized protein × 1 （Q936H5） MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Uncharacterized protein × 1 （Q936H5） MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–223； UniProt 94–313 Author chain C； PDBConstruct 4–223； UniProt 94–313

Uncharacterized protein

Staphylococcus aureus

UniProt Q936H5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P13051） MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P13051） MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q936H5_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–112； UniProt 1–112 Author chain D； PDBConstruct 1–112； UniProt 1–112

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	5ayr
Deposition date deposition_date	2015-09-02
Structure title title	The crystal structure of SAUGI/human UDG complex
Keywords keywords	DNA mimic protein, DNA mimicking, uracil-DNA glycosylase inhibitor, uracil-DNA glycosylase, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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.

5ayr__assembly_1__model_1

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

Download this curve (.dat)

5ayr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ayr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.15 Å
Rg (electron density)	20.11 Å
Total Rg	21.12 Å
Atom count	2742
Residues	333
Excluded volume	48925 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ayr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ayr__assembly_2__model_1`	dimeric （2）	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	Uracil-DNA glycosylase
Molecular weight formula_weight	26615.3 kDa
EC 编号 ec_number	3.2.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6002

MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKELLEHHHHHH

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	Uncharacterized protein
Molecular weight formula_weight	13367.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDTLHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTGGQ

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	518

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5ayra1
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

Domain ID domain_id	d5ayra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5ayra3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5ayrc1
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

Domain ID domain_id	d5ayrc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5ayrc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	5ayrA00
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

Domain ID domain_id	5ayrB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	5ayrC00
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

Domain ID domain_id	5ayrD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

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Unit-cell length a length_a	177.831 Å
Unit-cell length b length_b	52.853 Å
Unit-cell length c length_c	82.338 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.927 Å
R factor r_factor	0.1669
R_work r_work	0.1653
R_free r_free	0.1977

The crystal structure of SAUGI/human UDG complex

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

Uncharacterized 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

5ayr__assembly_1__model_1

5ayr__assembly_1__model_1 | I(q)

5ayr__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

The crystal structure of SAUGI/human UDG complex

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

Uncharacterized 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

5ayr__assembly_1__model_1

5ayr__assembly_1__model_1 | I(q)

5ayr__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)