4lzb

Uracil binding pocket in Vaccinia virus uracil DNA glycosylase

Method: X-RAY DIFFRACTION

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

Uracil-DNA glycosylase

Vaccinia virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	DIMETHYL SULFOXIDE × 2 POTASSIUM ION × 2 CHLORIDE ION × 3 1,2-ETHANEDIOL × 4 URACIL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	DIMETHYL SULFOXIDE × 4 POTASSIUM ION × 4 CHLORIDE ION × 5 1,2-ETHANEDIOL × 4 URACIL × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	POTASSIUM ION × 1 CHLORIDE ION × 2 1,2-ETHANEDIOL × 1 URACIL × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	DIMETHYL SULFOXIDE × 2 POTASSIUM ION × 1 CHLORIDE ION × 2 1,2-ETHANEDIOL × 2 URACIL × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	DIMETHYL SULFOXIDE × 2 POTASSIUM ION × 2 CHLORIDE ION × 2 1,2-ETHANEDIOL × 2 URACIL × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 3 URACIL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_VACCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–238； UniProt 1–218 Author chain B； PDBConstruct 21–238； UniProt 1–218 Author chain C； PDBConstruct 21–238； UniProt 1–218 Author chain D； PDBConstruct 21–238； UniProt 1–218 Author chain E； PDBConstruct 21–238； UniProt 1–218 Author chain F； PDBConstruct 21–238； UniProt 1–218 Author chain G； PDBConstruct 21–238； UniProt 1–218 Author chain H； PDBConstruct 21–238； UniProt 1–218 Author chain I； PDBConstruct 21–238； UniProt 1–218 Author chain J； PDBConstruct 21–238； UniProt 1–218 Author chain K； PDBConstruct 21–238； UniProt 1–218 Author chain L； PDBConstruct 21–238； UniProt 1–218

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	4lzb
Deposition date deposition_date	2013-07-31
Structure title title	Uracil binding pocket in Vaccinia virus uracil DNA glycosylase
Keywords keywords	alpha/beta DNA glycosylase fold, viral processivity factor, DNA binding component, DNA repair, A20, HYDROLASE; 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.

4lzb__assembly_1__model_1

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

Download this curve (.dat)

4lzb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lzb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.98 Å
Rg (electron density)	25.13 Å
Total Rg	25.91 Å
Atom count	3585
Residues	436
Excluded volume	64532 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lzb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lzb__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4lzb__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4lzb__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4lzb__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4lzb__assembly_6__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 (7)

Entity 1 Entity 1 polymer

Description description	Uracil-DNA glycosylase
Molecular weight formula_weight	27253.1 kDa
EC 编号 ec_number	3.2.2.27
Mutation mutation	D17N
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	23231

MGSSHHHHHHSSGLVPRGSHMNSVTVSHAPYTITYHNDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY

Source Source

Source organism organism	Vaccinia virus
Common name common_name	VACV
NCBI taxonomy ID ncbi_taxonomy_id	10245
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 non-polymer

Description description	URACIL
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1617

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4lzbA00
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	4lzbB00
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	4lzbC00
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	4lzbD00
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	4lzbE00
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	4lzbF00
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	4lzbG00
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	4lzbH00
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	4lzbI00
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	4lzbJ00
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	4lzbK00
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	4lzbL00
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	93.470 Å
Unit-cell length b length_b	114.045 Å
Unit-cell length c length_c	302.516 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	48

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	49.640 Å
R factor r_factor	0.2145
R_work r_work	0.2129
R_free r_free	0.2461

Uracil binding pocket in Vaccinia virus uracil DNA glycosylase

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

4lzb__assembly_1__model_1

4lzb__assembly_1__model_1 | I(q)

4lzb__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Uracil binding pocket in Vaccinia virus uracil DNA glycosylase

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

4lzb__assembly_1__model_1

4lzb__assembly_1__model_1 | I(q)

4lzb__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)