2zhx

Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

Method: X-RAY DIFFRACTION

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

Uracil-DNA glycosylase

Mycobacterium tuberculosis H37Rv

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） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase inhibitor × 1 （P14739） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase inhibitor × 1 （P14739） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase inhibitor × 1 （P14739） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase inhibitor × 1 （P14739） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase inhibitor × 1 （P14739） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase inhibitor × 1 （P14739） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–238； UniProt 1–227 Author chain C； PDBConstruct 12–238； UniProt 1–227 Author chain E； PDBConstruct 12–238； UniProt 1–227 Author chain G； PDBConstruct 12–238； UniProt 1–227 Author chain I； PDBConstruct 12–238； UniProt 1–227 Author chain K； PDBConstruct 12–238； UniProt 1–227 Author chain M； PDBConstruct 12–238； UniProt 1–227

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 （P67071） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P67071） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P67071） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P67071） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P67071） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P67071） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （P67071） 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 Author chain F； PDBConstruct 1–84； UniProt 1–84 Author chain H； PDBConstruct 1–84； UniProt 1–84 Author chain J； PDBConstruct 1–84； UniProt 1–84 Author chain L； PDBConstruct 1–84； UniProt 1–84 Author chain N； 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	2zhx
Deposition date deposition_date	2008-02-11
Structure title title	Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor
Keywords keywords	DNA repair, Ung-Ugi complex, Ung-DNA interactions, DNA damage, Glycosidase, Hydrolase, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/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.

2zhx__assembly_1__model_1

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

Download this curve (.dat)

2zhx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zhx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.13 Å
Rg (electron density)	18.85 Å
Total Rg	19.86 Å
Atom count	2354
Residues	307
Excluded volume	41913 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zhx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zhx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zhx__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2zhx__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2zhx__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2zhx__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2zhx__assembly_7__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 (3)

Entity 1 Entity 1 polymer

Description description	Uracil-DNA glycosylase
Molecular weight formula_weight	25813.5 kDa
EC 编号 ec_number	3.2.2.3
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M
Atom count atom_count	16840

MHHHHHHGMASMTARPLSELVERGWAAALEPVADQVAHMGQFLRAEIAAGRRYLPAGSNVLRAFTFPFDNVRVLIVGQDPYPTPGHAVGLSFSVAPDVRPWPRSLANIFDEYTADLGYPLPSNGDLTPWAQRGVLLLNRVLTVRPSNPASHRGKGWEAVTECAIRALAARAAPLVAILWGRDASTLKPMLAAGNCVAIESPHPSPLSASRGFFGSRPFSRANELLVGMGAEPIDWRLP

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

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	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N

MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML

Source Source

Source organism organism	Bacillus phage PBS2
NCBI taxonomy ID ncbi_taxonomy_id	10684
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d2zhxa_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxb_
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	d2zhxc_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxd_
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	d2zhxe_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxf_
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	d2zhxg_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxh_
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	d2zhxi_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxj_
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	d2zhxk_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxl_
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	d2zhxm_
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.18.1.0 — automated matches

Domain ID domain_id	d2zhxn_
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 (14 domains)

Domain ID domain_id	2zhxA00
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	2zhxB00
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	2zhxC00
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	2zhxD00
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	2zhxE00
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	2zhxF00
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	2zhxG00
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	2zhxH00
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	2zhxI00
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	2zhxJ00
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	2zhxK00
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	2zhxL00
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	2zhxM00
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	2zhxN00
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	201.143 Å
Unit-cell length b length_b	64.274 Å
Unit-cell length c length_c	203.677 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2358
R_work r_work	0.2337
R_free r_free	0.2764

Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

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

2zhx__assembly_1__model_1

2zhx__assembly_1__model_1 | I(q)

2zhx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (3)

Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

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

2zhx__assembly_1__model_1

2zhx__assembly_1__model_1 | I(q)

2zhx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. Citations (3)