5cdn

2.8A structure of etoposide with S.aureus DNA gyrase and DNA

Method: X-RAY DIFFRACTION

▼

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

DNA gyrase subunit A

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA gyrase subunit B,DNA gyrase subunit B × 2 （P66937） ;DNA (5'-D(PGPAPGPCPGPTPAPGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 ;DNA (5'-D(PGPAPGPCPGPTPAPCGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 SULFATE ION × 1 MANGANESE (II) ION × 2 GLYCEROL × 3 SODIUM ION × 1 ;(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside ; × 2 water × 8	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA gyrase subunit B,DNA gyrase subunit B × 2 （P66937） ;DNA (5'-D(PGPAPGPCPGPTPAPGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 ;DNA (5'-D(PGPAPGPCPGPTPAPCGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 MANGANESE (II) ION × 2 GLYCEROL × 1 ;(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside ; × 2 water × 8	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–481； UniProt 10–490 Author chain C； PDBConstruct 1–481； UniProt 10–490 Author chain R； PDBConstruct 1–481； UniProt 10–490 Author chain T； PDBConstruct 1–481； UniProt 10–490

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus (strain N315)

UniProt P66937

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA gyrase subunit A × 2 （Q99XG5） ;DNA (5'-D(PGPAPGPCPGPTPAPGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 ;DNA (5'-D(PGPAPGPCPGPTPAPCGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 SULFATE ION × 1 MANGANESE (II) ION × 2 GLYCEROL × 3 SODIUM ION × 1 ;(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside ; × 2 water × 8	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA gyrase subunit A × 2 （Q99XG5） ;DNA (5'-D(PGPAPGPCPGPTPAPGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 ;DNA (5'-D(PGPAPGPCPGPTPAPCGPGPCPCPGPTPAPCPGPCPTPC)-3') ; × 2 MANGANESE (II) ION × 2 GLYCEROL × 1 ;(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside ; × 2 water × 8	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–127； UniProt 417–543 Author chain B； PDBConstruct 130–189； UniProt 580–639 Author chain D； PDBConstruct 1–127； UniProt 417–543 Author chain D； PDBConstruct 130–189； UniProt 580–639 Author chain S； PDBConstruct 1–127； UniProt 417–543 Author chain S； PDBConstruct 130–189； UniProt 580–639 Author chain U； PDBConstruct 1–127； UniProt 417–543 Author chain U； PDBConstruct 130–189； UniProt 580–639

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5cdn
Deposition date deposition_date	2015-07-04
Structure title title	2.8A structure of etoposide with S.aureus DNA gyrase and DNA
Keywords keywords	TYPE IIA TOPOISOMERASE, ANTIBACTERIAL, INHIBITOR, isomerase; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5cdn__assembly_1__model_1

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

Download this curve (.dat)

5cdn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cdn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.60 Å
Rg (electron density)	37.40 Å
Total Rg	37.73 Å
Atom count	11316
Residues	1374
Excluded volume	198130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cdn__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5cdn__assembly_2__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	DNA gyrase subunit A
Molecular weight formula_weight	54664.2 kDa
EC 编号 ec_number	5.99.1.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,R,T
Atom count atom_count	23069

NERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL

Source Source

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

Entity 2 Entity 2 polymer

Description description	DNA gyrase subunit B,DNA gyrase subunit B
Molecular weight formula_weight	21274.2 kDa
EC 编号 ec_number	5.99.1.3,5.99.1.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,S,U

KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVY

Source Source

Source organism organism	Staphylococcus aureus (strain N315)
NCBI taxonomy ID ncbi_taxonomy_id	158879
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPAPGPCPGPTPAPGPGPCPCPGPTPAPCPGPCPTPC)-3') ;
Molecular weight formula_weight	2451.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,V,W

GAGCGTAC

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PGPAPGPCPGPTPAPCGPGPCPCPGPTPAPCPGPCPTPC)-3') ;
Molecular weight formula_weight	3639.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,O,N,P

GGCCGTACGCTC

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	;(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside ;
Molecular weight formula_weight	588.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	412

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5cdnB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

Domain ID domain_id	5cdnD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

Domain ID domain_id	5cdnS01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

Domain ID domain_id	5cdnU01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

▶

Unit-cell length a length_a	89.782 Å
Unit-cell length b length_b	170.081 Å
Unit-cell length c length_c	124.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	39.350 Å
R factor r_factor	0.2143
R_work r_work	0.2132
R_free r_free	0.2420

2.8A structure of etoposide with S.aureus DNA gyrase and DNA

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

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 B

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

5cdn__assembly_1__model_1

5cdn__assembly_1__model_1 | I(q)

5cdn__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer 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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

2.8A structure of etoposide with S.aureus DNA gyrase and DNA

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

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 B

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

5cdn__assembly_1__model_1

5cdn__assembly_1__model_1 | I(q)

5cdn__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer 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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)