SAXSdb — 6lye

▼

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

Probable uracil-DNA glycosylase

Acanthamoeba polyphaga mimivirus

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）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_MIMIV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 95–370

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	Probable uracil-DNA glycosylase × 1 （Q5UPT2）	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 I； PDBConstruct 1–83； UniProt 2–84

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6lye
Deposition date deposition_date	2020-02-14
Structure title title	Crystal Structure of mimivirus UNG Y322F in complex with UGI
Keywords keywords	UDG, UNG, uracil DNA glycosylase, UGI, DNA BINDING PROTEIN-INHIBITOR complex; DNA BINDING PROTEIN/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.

6lye__assembly_1__model_1

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

Download this curve (.dat)

6lye__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6lye__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.10 Å
Rg (electron density)	19.87 Å
Total Rg	20.89 Å
Atom count	2851
Residues	353
Excluded volume	51190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6lye__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Description description	Probable uracil-DNA glycosylase
Molecular weight formula_weight	31831.7 kDa
EC 编号 ec_number	3.2.2.-
Mutation mutation	Y322F
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2851

NRIITEYILIDANNYHFKSWIECFPDCKVNLKLLLFRPEWFDFFKYVESKTYFPQLESKLSSYLEKRQRIVPYPELLFNTMNVLPPGKIKVVILGQDPYPGSCISGVPYAMGCSFSVPLNCPVPKSLANIYTNLIKFNHMRKAPKHGCLASWILQGTFMINSAFTTVLNESGVHARTWESFTADLIDYLTDNYDDLIFVAWGAHAHKLCQRVDPKKHYIITSSHPSPFSVSNTMTSMSYGPNPKKVTYPSFNSVDHFGKINEHLKSRNKKPIFWDL

Source Source

Source organism organism	Acanthamoeba polyphaga mimivirus
Common name common_name	APMV
NCBI taxonomy ID ncbi_taxonomy_id	212035
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Uracil-DNA glycosylase inhibitor
Molecular weight formula_weight	9351.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

TNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML

Source Source

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

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6lyei_
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 (2 domains)

Domain ID domain_id	6lyeA01
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	6lyeI00
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

▶

Unit-cell length a length_a	104.230 Å
Unit-cell length b length_b	104.230 Å
Unit-cell length c length_c	83.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	45.133 Å
R factor r_factor	0.1868
R_work r_work	0.1732
R_free r_free	0.2085

Crystal Structure of mimivirus UNG Y322F in complex with UGI

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

Probable 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

6lye__assembly_1__model_1

6lye__assembly_1__model_1 | I(q)

6lye__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of mimivirus UNG Y322F in complex with UGI

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

Probable 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

6lye__assembly_1__model_1

6lye__assembly_1__model_1 | I(q)

6lye__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)