6z1a

Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 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 A

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 4	;DNA (5'-D(APGPCPCPGPTPAPG)-3') ; × 2 ;DNA (5'-D(PGPTPAPCPCPTPAPCPGPGPCPT)-3') ; × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 MANGANESE (II) ION × 4 DIMETHYL SULFOXIDE × 3 CHLORIDE ION × 1 ~{N}-[(4-chlorophenyl)methyl]-1-[2-(6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-amine × 1 water × 6	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
Chains and sequence ranges	Author chain B； PDBConstruct 2–202； UniProt 410–644 Author chain D； PDBConstruct 2–202； UniProt 410–644

DNA gyrase subunit B,DNA gyrase subunit A

Staphylococcus aureus

UniProt P20831

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 4	;DNA (5'-D(APGPCPCPGPTPAPG)-3') ; × 2 ;DNA (5'-D(PGPTPAPCPCPTPAPCPGPGPCPT)-3') ; × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 MANGANESE (II) ION × 4 DIMETHYL SULFOXIDE × 3 CHLORIDE ION × 1 ~{N}-[(4-chlorophenyl)methyl]-1-[2-(6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-amine × 1 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GYRA_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 203–692； UniProt 2–491 Author chain D； PDBConstruct 203–692； UniProt 2–491

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	6z1a
Deposition date deposition_date	2020-05-13
Structure title title	Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA
Keywords keywords	TYPE IIA TOPOISOMERASE, ANTIBACTERIAL, INHIBITOR, ISOMERASE, FUSION PROTEIN; ISOMERASE
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.

6z1a__assembly_1__model_1

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

Download this curve (.dat)

6z1a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z1a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.90 Å
Rg (electron density)	36.69 Å
Total Rg	37.06 Å
Atom count	11425
Residues	1382
Excluded volume	200370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z1a__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Description description	DNA gyrase subunit B,DNA gyrase subunit A
Molecular weight formula_weight	78079.0 kDa
EC 编号 ec_number	5.6.2.2,5.6.2.2
Mutation mutation	Y1123F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	11802

MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELEAILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APGPCPCPGPTPAPG)-3') ;
Molecular weight formula_weight	2451.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F

AGCCGTAG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPTPAPCPCPTPAPCPGPGPCPT)-3') ;
Molecular weight formula_weight	3638.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,H

GTACCTACGGCT

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	~{N}-[(4-chlorophenyl)methyl]-1-[2-(6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-amine
Molecular weight formula_weight	410.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6z1aB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6z1aD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	92.592 Å
Unit-cell length b length_b	92.592 Å
Unit-cell length c length_c	405.464 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	80.320 Å
R factor r_factor	0.1810
R_work r_work	0.1790
R_free r_free	0.2167

Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA

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

DNA gyrase subunit B,DNA gyrase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

DNA gyrase subunit B,DNA gyrase subunit A

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

6z1a__assembly_1__model_1

6z1a__assembly_1__model_1 | I(q)

6z1a__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA

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

DNA gyrase subunit B,DNA gyrase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA gyrase subunit B,DNA gyrase subunit A

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

6z1a__assembly_1__model_1

6z1a__assembly_1__model_1 | I(q)

6z1a__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)