3dho

Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor

Method: X-RAY DIFFRACTION

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

Streptogramin A acetyltransferase

Enterococcus faecium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	DIMETHYL SULFOXIDE × 5 6-bromo-N'-[(1Z)-(3,5-dichloro-2-hydroxyphenyl)methylidene]-2-methylquinoline-4-carbohydrazide × 3 FORMIC ACID × 5 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	DIMETHYL SULFOXIDE × 1 6-bromo-N'-[(1Z)-(3,5-dichloro-2-hydroxyphenyl)methylidene]-2-methylquinoline-4-carbohydrazide × 3 FORMIC ACID × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_ENTFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 1–209 Author chain B； PDBConstruct 1–209； UniProt 1–209 Author chain C； PDBConstruct 1–209； UniProt 1–209 Author chain D； PDBConstruct 1–209； UniProt 1–209 Author chain E； PDBConstruct 1–209； UniProt 1–209 Author chain F； PDBConstruct 1–209； UniProt 1–209

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	3dho
Deposition date deposition_date	2008-06-18
Structure title title	Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor
Keywords keywords	Streptogramin Acetyltransferase Left-Handed Parallel Beta Helix, Acyltransferase, Antibiotic resistance, Transferase; TRANSFERASE
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.

3dho__assembly_2__model_1

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

Download this curve (.dat)

3dho__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dho__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.59 Å
Rg (electron density)	26.56 Å
Total Rg	27.23 Å
Atom count	4921
Residues	609
Excluded volume	88446 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dho__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dho__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Streptogramin A acetyltransferase
Molecular weight formula_weight	23675.3 kDa
EC 编号 ec_number	2.3.1.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	11211

MGPNPMKMYPIEGNKSVQFIKPILEKLENVEVGEYSYYDSKNGETFDKQILYHYPILNDKLKIGKFCSIGPGVTIIMNGANHRMDGSTYPFNLFGNGWEKHMPKLDQLPIKGDTIIGNDVWIGKDVVIMPGVKIGDGAIVAANSVVVKDIAPYMLAGGNPANEIKQRFDQDTINQLLDIKWWNWPIDIINENIDKILDNSIIREVIWKK

Source Source

Source organism organism	Enterococcus faecium
Common name common_name	Streptococcus faecium
NCBI taxonomy ID ncbi_taxonomy_id	1352
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	6

Entity 3 Entity 3 non-polymer

Description description	6-bromo-N'-[(1Z)-(3,5-dichloro-2-hydroxyphenyl)methylidene]-2-methylquinoline-4-carbohydrazide
Molecular weight formula_weight	453.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1350

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3dhoa_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.3 — Galactoside acetyltransferase-like

Domain ID domain_id	d3dhob_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.3 — Galactoside acetyltransferase-like

Domain ID domain_id	d3dhoc_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.3 — Galactoside acetyltransferase-like

Domain ID domain_id	d3dhod_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.3 — Galactoside acetyltransferase-like

Domain ID domain_id	d3dhoe_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.3 — Galactoside acetyltransferase-like

Domain ID domain_id	d3dhof_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.3 — Galactoside acetyltransferase-like

CATH v4.4 (6 domains)

Domain ID domain_id	3dhoA00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3dhoB00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3dhoC00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3dhoD00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3dhoE00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3dhoF00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	183.653 Å
Unit-cell length b length_b	183.620 Å
Unit-cell length c length_c	183.644 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	96

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	25.470 Å
R factor r_factor	0.1779
R_work r_work	0.1760
R_free r_free	0.2132

Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor

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

Streptogramin A acetyltransferase

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

3dho__assembly_2__model_1

3dho__assembly_2__model_1 | I(q)

3dho__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor

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

Streptogramin A acetyltransferase

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

3dho__assembly_2__model_1

3dho__assembly_2__model_1 | I(q)

3dho__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)