SAXSdb — 2vbq

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

;AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE ;

SALMONELLA CHOLERAESUIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;(3R,9Z)-17-[(2R,3S,4R,5R,6R)-5-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-yl]-3-hydroxy-2,2-dimethyl-4,8,15-trioxo-12-thia-5,9,16-triazaheptadec-9-en-1-yl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 NICKEL (II) ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9R381_SALEN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–165； UniProt 1–145 Author chain B； PDBConstruct 21–165； UniProt 1–145

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	2vbq
Deposition date deposition_date	2007-09-14
Structure title title	Structure of AAC(6')-Iy in complex with bisubstrate analog CoA-S- monomethyl-acetylneamine.
Keywords keywords	AMINOGLYCOSIDE, ACETYLTRANSFERASE, DRUG RESISTANCE, BISUBSTRATE INHIBITOR, 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.

2vbq__assembly_1__model_1

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

Download this curve (.dat)

2vbq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vbq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.63 Å
Rg (electron density)	20.90 Å
Total Rg	21.81 Å
Atom count	2465
Residues	291
Excluded volume	43029 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vbq__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	;AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE ;
Molecular weight formula_weight	18556.9 kDa
EC 编号 ec_number	2.3.1.82
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2684

MGSSHHHHHHSSGLVPRGSHMDIRQMNKTHLEHWRGLRKQLWPGHPDDAHLADGEEILQADHLASFIAMADGVAIGFADASIRHDYVNGCDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCREMASDTSPENTISQKVHQALGFEETERVIFYRKRC

Source Source

Source organism organism	SALMONELLA CHOLERAESUIS
NCBI taxonomy ID ncbi_taxonomy_id	591
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;(3R,9Z)-17-[(2R,3S,4R,5R,6R)-5-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-yl]-3-hydroxy-2,2-dimethyl-4,8,15-trioxo-12-thia-5,9,16-triazaheptadec-9-en-1-yl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate ;
Molecular weight formula_weight	1141.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2vbqa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d2vbqa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2vbqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

CATH v4.4 (2 domains)

Domain ID domain_id	2vbqA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	2vbqB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

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Unit-cell length a length_a	84.964 Å
Unit-cell length b length_b	44.599 Å
Unit-cell length c length_c	88.387 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	88.050 Å
R factor r_factor	0.1830
R_work r_work	0.1810
R_free r_free	0.2300

Structure of AAC(6')-Iy in complex with bisubstrate analog CoA-S- monomethyl-acetylneamine.

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

;AMINOGLYCOSIDE 6'-N-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

2vbq__assembly_1__model_1

2vbq__assembly_1__model_1 | I(q)

2vbq__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 (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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of AAC(6')-Iy in complex with bisubstrate analog CoA-S- monomethyl-acetylneamine.

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

;AMINOGLYCOSIDE 6'-N-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

2vbq__assembly_1__model_1

2vbq__assembly_1__model_1 | I(q)

2vbq__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 (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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)