SAXSdb — 2j8x

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

URACIL-DNA GLYCOSYLASE

EPSTEIN-BARR VIRUS

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 INHIBITOR × 1 （P14739） UREA × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	URACIL-DNA GLYCOSYLASE INHIBITOR × 1 （P14739） UREA × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q777D9_EBVG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 25–255 Author chain C； PDBConstruct 1–231； UniProt 25–255

URACIL-DNA GLYCOSYLASE INHIBITOR

BACILLUS PHAGE PBS2

UniProt P14739

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 （Q777D9） UREA × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	URACIL-DNA GLYCOSYLASE × 1 （Q777D9） UREA × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNGI_BPPB2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–84； UniProt 1–84 Author chain D； PDBConstruct 1–84； UniProt 1–84

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	2j8x
Deposition date deposition_date	2006-10-31
Structure title title	Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2
Keywords keywords	;HYDROLASE-INHIBITOR COMPLEX, EBV, DNA REPAIR, LYTIC PROTEIN, EPSTEIN-BARR VIRUS, URACIL- DNA GLYCOSYLASE, HYDROLASE, URACIL-DNA GLYCOSYLASE 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.

2j8x__assembly_1__model_1

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

Download this curve (.dat)

2j8x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j8x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.39 Å
Rg (electron density)	19.18 Å
Total Rg	20.20 Å
Atom count	2471
Residues	313
Excluded volume	44163 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j8x__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j8x__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	25758.7 kDa
EC 编号 ec_number	3.2.2.3
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	5307

GENLLLPDLWLDFLQLSPIFQRKLAAVIACVRRLRTQATVYPEEDMCMAWARFCDPSDIKVVILGQDPYHGGQANGLAFSVAYGFPVPPSLRNIYAELHRSLPEFSPPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSERLKACVFMLWGAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLANNFLREKGLGEIDWRL

Source Source

Source organism organism	EPSTEIN-BARR VIRUS
Common name common_name	HHV-4
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	URACIL-DNA GLYCOSYLASE INHIBITOR
Molecular weight formula_weight	9482.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML

Source Source

Source organism organism	BACILLUS PHAGE PBS2
NCBI taxonomy ID ncbi_taxonomy_id	10684
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	UREA
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	389

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2j8xa1
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	d2j8xb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.5 — Uracil-DNA glycosylase inhibitor protein
Family Family family	d.17.5.1 — Uracil-DNA glycosylase inhibitor protein

Domain ID domain_id	d2j8xc_
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	d2j8xd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.5 — Uracil-DNA glycosylase inhibitor protein
Family Family family	d.17.5.1 — Uracil-DNA glycosylase inhibitor protein

CATH v4.4 (4 domains)

Domain ID domain_id	2j8xA00
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	2j8xB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	20 — Bacteriophage PBS2, uracil-glycosylase inhibitor

Domain ID domain_id	2j8xC00
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	2j8xD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	20 — Bacteriophage PBS2, uracil-glycosylase inhibitor

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Unit-cell length a length_a	62.406 Å
Unit-cell length b length_b	82.942 Å
Unit-cell length c length_c	269.130 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	49.880 Å
R factor r_factor	0.1960
R_work r_work	0.1930
R_free r_free	0.2570

Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2

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

URACIL-DNA GLYCOSYLASE INHIBITOR

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

2j8x__assembly_1__model_1

2j8x__assembly_1__model_1 | I(q)

2j8x__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2

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

URACIL-DNA GLYCOSYLASE INHIBITOR

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

2j8x__assembly_1__model_1

2j8x__assembly_1__model_1 | I(q)

2j8x__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)