SAXSdb — 5nnu

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

Uracil-DNA glycosylase

Human herpesvirus 8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	DNA containing an abasic site × 1 DNA × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	DNA containing an abasic site × 1 DNA × 1 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	DNA containing an abasic site × 1 DNA × 1 water × 3	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	DNA containing an abasic site × 1 DNA × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q76RG8_HHV8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–240； UniProt 19–255 Author chain B； PDBConstruct 4–240； UniProt 19–255 Author chain D； PDBConstruct 4–240； UniProt 19–255 Author chain E； PDBConstruct 4–240； UniProt 19–255

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	5nnu
Deposition date deposition_date	2017-04-10
Structure title title	KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping
Keywords keywords	Uracil-DNA glycosylase, 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.

5nnu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5nnu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nnu__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.19 Å
Rg (electron density)	18.83 Å
Total Rg	19.80 Å
Atom count	2223
Residues	251
Excluded volume	38300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nnu__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5nnu__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5nnu__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5nnu__assembly_4__model_1`	trimeric （3）	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	DNA containing an abasic site
Molecular weight formula_weight	3230.1 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	S,U,W,Y
Atom count atom_count	8844

AATGTXATCTT

Entity 2 Entity 2 polymer

Description description	Uracil-DNA glycosylase
Molecular weight formula_weight	27226.2 kDa
EC 编号 ec_number	3.2.2.27
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SASGVDDRDLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTTVYPPQDKLMWWSHCCDPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELEASVPNFSTPSHGCLDSWARQGVLLLNTVLTVEKGRAGSHEGLGWDWFTSFIISSISSKLEHCVFLLWGRKAIDRTPLINAQKHLVLTAQHPSPLASLGGRHSRWPRFQGCNHFNLANDYLTRHRRETVDWGLLEQ

Source Source

Source organism organism	Human herpesvirus 8
NCBI taxonomy ID ncbi_taxonomy_id	37296
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA
Molecular weight formula_weight	3365.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T,V,X,Z

AAGATAACATT

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5nnuA00
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	5nnuB00
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	5nnuD00
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	5nnuE00
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	82.100 Å
Unit-cell length b length_b	70.800 Å
Unit-cell length c length_c	140.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.970 Å
Low-resolution limit resolution_low	49.200 Å
R factor r_factor	0.2451
R_work r_work	0.2438
R_free r_free	0.2692

KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping

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

5nnu__assembly_2__model_1

5nnu__assembly_2__model_1 | I(q)

5nnu__assembly_2__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping

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

5nnu__assembly_2__model_1

5nnu__assembly_2__model_1 | I(q)

5nnu__assembly_2__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)