6qx2

3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus

UniProt P0A0K8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
3 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
4 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
5 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q6GKU0) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
6 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q2FKQ1) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name GYRB_STAAU
Isoform —
PDB entities 1, 3
Chains and sequence ranges Author chain B; PDBConstruct 1–128; UniProt 416–543 Author chain S; PDBConstruct 1–128; UniProt 416–543 Author chain b; PDBConstruct 1–128; UniProt 416–543 Author chain s; PDBConstruct 1–128; UniProt 416–543 Author chain D; PDBConstruct 1–127; UniProt 417–543 Author chain U; PDBConstruct 1–127; UniProt 417–543 Author chain m; PDBConstruct 1–127; UniProt 417–543

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus

UniProt P66936

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
3 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
4 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
6 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q2FKQ1) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name GYRB_STAAM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 129–186; UniProt 581–638 Author chain S; PDBConstruct 129–186; UniProt 581–638 Author chain b; PDBConstruct 129–186; UniProt 581–638 Author chain s; PDBConstruct 129–186; UniProt 581–638

DNA gyrase subunit A

Staphylococcus aureus

UniProt Q99XG5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
2 Insufficient information Heteromer Protein 4 DNA 2 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q2FKQ1) DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q2FKQ1) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
3 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
4 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
5 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q6GKU0) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
6 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P66937,Q2FKQ1) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name GYRA_STAAN
Isoform —
PDB entities 2, 6
Chains and sequence ranges Author chain A; PDBConstruct 1–490; UniProt 2–491 Author chain C; PDBConstruct 1–490; UniProt 2–491 Author chain L; PDBConstruct 1–490; UniProt 2–491 Author chain R; PDBConstruct 1–490; UniProt 2–491 Author chain T; PDBConstruct 1–490; UniProt 2–491 Author chain a; PDBConstruct 1–490; UniProt 2–491 Author chain c; PDBConstruct 1–490; UniProt 2–491 Author chain j; PDBConstruct 1–490; UniProt 2–491 Author chain l; PDBConstruct 1–490; UniProt 2–491 Author chain r; PDBConstruct 1–490; UniProt 2–491 Author chain t; PDBConstruct 1–490; UniProt 2–491 Author chain J; PDBConstruct 1–480; UniProt 11–491

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus

UniProt Q6GKU0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
3 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
4 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
5 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name GYRB_STAAR
Isoform —
PDB entities 3, 9, 11
Chains and sequence ranges Author chain D; PDBConstruct 130–188; UniProt 580–638 Author chain U; PDBConstruct 130–188; UniProt 580–638 Author chain m; PDBConstruct 130–188; UniProt 580–638 Author chain d; PDBConstruct 130–181; UniProt 586–637 Author chain k; PDBConstruct 129–188; UniProt 581–640

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus

UniProt P66937

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
2 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 1 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 DNA gyrase subunit A × 1 (Q99XG5) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
4 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
5 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 (Q99XG5) DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,Q6GKU0) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 1 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
6 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name GYRB_STAAN
Isoform —
PDB entities 5, 7, 9, 11, 12
Chains and sequence ranges Author chain K; PDBConstruct 1–128; UniProt 416–543 Author chain M; PDBConstruct 1–127; UniProt 417–543 Author chain d; PDBConstruct 1–127; UniProt 417–543 Author chain k; PDBConstruct 1–128; UniProt 416–543 Author chain u; PDBConstruct 1–127; UniProt 417–543

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus

UniProt Q2FKQ1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
2 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 1 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 DNA gyrase subunit A × 1 (Q99XG5) (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers
6 Insufficient information Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 1 (P0A0K8,P66936) DNA gyrase subunit A × 2 (Q99XG5) ;DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name GYRB_STAA3
Isoform —
PDB entities 5, 7, 12
Chains and sequence ranges Author chain K; PDBConstruct 129–187; UniProt 581–639 Author chain M; PDBConstruct 130–189; UniProt 580–639 Author chain u; PDBConstruct 130–187; UniProt 580–637

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_id6qx2
Deposition date deposition_date2019-03-06
Structure title title3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA
Keywords keywordsInhibitor, DNA complex, isomerase; ISOMERASE
Experimental Method methodX-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.

6qx2__assembly_1__model_1

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

Download this curve (.dat)

6qx2__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6qx2__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)37.00 Å
Rg (electron density)36.77 Å
Total Rg37.11 Å
Atom count11117
Residues1374
Excluded volume194240 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6qx2__assembly_1__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6qx2__assembly_2__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6qx2__assembly_3__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6qx2__assembly_4__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 6qx2__assembly_5__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 6qx2__assembly_6__model_1 hexameric (6) 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 (13)

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7. Citations (1)