6lyv

The crystal structure of SAUGI/KSHVUDG complex

Method: X-RAY DIFFRACTION

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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 heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	SAUGI × 1 （Q936H5） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q76RG8_HHV8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–255； UniProt 1–255 Author chain C； PDBConstruct 1–255； UniProt 1–255 Author chain E； PDBConstruct 1–255； UniProt 1–255 Author chain G； PDBConstruct 1–255； UniProt 1–255 Author chain I； PDBConstruct 1–255； UniProt 1–255 Author chain K； PDBConstruct 1–255； UniProt 1–255 Author chain M； PDBConstruct 1–255； UniProt 1–255 Author chain O； PDBConstruct 1–255； UniProt 1–255

SAUGI

Staphylococcus aureus

UniProt Q936H5

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 （Q76RG8） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q76RG8） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q936H5_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–112； UniProt 1–112 Author chain D； PDBConstruct 1–112； UniProt 1–112 Author chain F； PDBConstruct 1–112； UniProt 1–112 Author chain H； PDBConstruct 1–112； UniProt 1–112 Author chain J； PDBConstruct 1–112； UniProt 1–112 Author chain L； PDBConstruct 1–112； UniProt 1–112 Author chain N； PDBConstruct 1–112； UniProt 1–112 Author chain P； PDBConstruct 1–112； UniProt 1–112

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	6lyv
Deposition date deposition_date	2020-02-16
Structure title title	The crystal structure of SAUGI/KSHVUDG complex
Keywords keywords	DNA mimic protein, uracil-DNA glycosylase inhibitor, uracil-DNA glycosylase, DNA repair, herpesvirus, 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.

6lyv__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6lyv__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6lyv__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	21.23 Å
Rg (electron density)	20.08 Å
Total Rg	21.09 Å
Atom count	2724
Residues	333
Excluded volume	48612 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6lyv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6lyv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6lyv__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6lyv__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6lyv__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6lyv__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6lyv__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`6lyv__assembly_8__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	29045.3 kDa
EC 编号 ec_number	3.2.2.27
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	22519

MDAWLQQTVFRGTLSISQGVDDRDLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTTVYPPQDKLMWWSHCCDPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELEASVPNFSTPSHGCLDSWARQGVLLLNTVLTVEKGRAGSHEGLGWDWFTSFIISSISSKLEHCVFLLWGRKAIDRTPLINAQKHLVLTAQHPSPLASLGGRHSRWPRFQGCNHFNLANDYLTRHRRETVDWGLLEQ

Source Source

Source organism organism	Human herpesvirus 8
Common name common_name	HHV-8,Human gammaherpesvirus 8
NCBI taxonomy ID ncbi_taxonomy_id	37296
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SAUGI
Molecular weight formula_weight	13367.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

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

MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDTLHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTGGQ

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	782

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	6lyvA00
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	6lyvB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvC00
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	6lyvD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvE00
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	6lyvF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvG00
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	6lyvH01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvI00
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	6lyvJ01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvK00
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	6lyvL01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvM00
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	6lyvN01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

Domain ID domain_id	6lyvO00
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	6lyvP01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	250 — S. aureus uracil DNA glycosylase inhibitor

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Unit-cell length a length_a	85.887 Å
Unit-cell length b length_b	92.196 Å
Unit-cell length c length_c	98.107 Å
Unit-cell angle α angle_alpha	108.14 °
Unit-cell angle β angle_beta	90.61 °
Unit-cell angle γ angle_gamma	92.23 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.1938
R_work r_work	0.1918
R_free r_free	0.2315

The crystal structure of SAUGI/KSHVUDG complex

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

SAUGI

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

6lyv__assembly_6__model_1

6lyv__assembly_6__model_1 | I(q)

6lyv__assembly_6__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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

The crystal structure of SAUGI/KSHVUDG complex

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

SAUGI

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

6lyv__assembly_6__model_1

6lyv__assembly_6__model_1 | I(q)

6lyv__assembly_6__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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)