SAXSdb — 4l5n

▼

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

Uracil-DNA glycosylase

Herpes simplex virus type 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Early protein GP1B × 2 （P06948） ACETATE ION × 9 water × 3	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACETATE ION × 7 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Early protein GP1B × 2 （P06948） ACETATE ION × 6 water × 3	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 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 3–241； UniProt 96–334 Author chain B； PDBConstruct 3–241； UniProt 96–334

Early protein GP1B

Bacillus phage PZA

UniProt P06948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Uracil-DNA glycosylase × 1 （P10186） ACETATE ION × 9 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Uracil-DNA glycosylase × 1 （P10186） ACETATE ION × 6 water × 3	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VG1B_BPPZA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–55； UniProt 2–56 Author chain D； PDBConstruct 1–55； UniProt 2–56 Author chain E； PDBConstruct 1–55； UniProt 2–56 Author chain F； PDBConstruct 1–55； UniProt 2–56

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4l5n
Deposition date deposition_date	2013-06-11
Structure title title	Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus phage PZA inhibitor protein p56
Keywords keywords	UDG Inhibition, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4l5n__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4l5n__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4l5n__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	15.04 Å
Rg (electron density)	13.58 Å
Total Rg	14.73 Å
Atom count	818
Residues	99
Excluded volume	14525 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4l5n__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4l5n__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4l5n__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4l5n__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4l5n__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4l5n__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Uracil-DNA glycosylase
Molecular weight formula_weight	26980.0 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,B
Atom count atom_count	5681

STGGVSPAATSAPLDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWSV

Source Source

Source organism organism	Herpes simplex virus type 1
NCBI taxonomy ID ncbi_taxonomy_id	10299
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Early protein GP1B
Molecular weight formula_weight	6455.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F

VQNDFLDSYDVTMLLQDDNGKQYYEYHKGLSLSDFEVLYGNTVDEIIKLRVDKIS

Source Source

Source organism organism	Bacillus phage PZA
NCBI taxonomy ID ncbi_taxonomy_id	10757
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	409

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4l5na_
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	d4l5nb_
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 (6 domains)

Domain ID domain_id	4l5nA00
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	4l5nB00
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	4l5nC00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	250 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4l5nD00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	250 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4l5nE00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	250 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4l5nF00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	250 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	30 —

▶

Unit-cell length a length_a	52.704 Å
Unit-cell length b length_b	91.375 Å
Unit-cell length c length_c	162.862 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1725
R_work r_work	0.1710
R_free r_free	0.2018

Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus phage PZA inhibitor protein p56

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

Early protein GP1B

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

4l5n__assembly_5__model_1

4l5n__assembly_5__model_1 | I(q)

4l5n__assembly_5__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 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus phage PZA inhibitor protein p56

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

Early protein GP1B

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

4l5n__assembly_5__model_1

4l5n__assembly_5__model_1 | I(q)

4l5n__assembly_5__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 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)