SAXSdb — 5d7c

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

DNA gyrase subunit B

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(4S)-2-METHYL-2,4-PENTANEDIOL × 2 1-ethyl-3-[1-(pyridin-2-yl)-6-(pyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-3-yl]urea × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(4S)-2-METHYL-2,4-PENTANEDIOL × 2 1-ethyl-3-[1-(pyridin-2-yl)-6-(pyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-3-yl]urea × 1 MAGNESIUM ION × 7 water × 1	Consistent with protein count

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 A； PDBConstruct 3–212； UniProt 2–234 Author chain B； PDBConstruct 3–212； UniProt 2–234

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	5d7c
Deposition date deposition_date	2015-08-13
Structure title title	Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand
Keywords keywords	DNA gyrase, GyrB, ligand, structure-based design, ISOMERASE-ISOMERASE INHIBITOR complex; ISOMERASE/ISOMERASE INHIBITOR
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.

5d7c__assembly_2__model_1

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

Download this curve (.dat)

5d7c__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5d7c__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.71 Å
Rg (electron density)	16.34 Å
Total Rg	17.42 Å
Atom count	1549
Residues	186
Excluded volume	27402 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5d7c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5d7c__assembly_2__model_1`	monomeric （1）	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	DNA gyrase subunit B
Molecular weight formula_weight	23931.6 kDa
EC 编号 ec_number	5.99.1.3
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	3586

GSVTALSDVNNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGGIK

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1-ethyl-3-[1-(pyridin-2-yl)-6-(pyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-3-yl]urea
Molecular weight formula_weight	358.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	342

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5d7ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.0 — automated matches

Domain ID domain_id	d5d7cb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5d7cA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	5d7cB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

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Unit-cell length a length_a	142.803 Å
Unit-cell length b length_b	55.485 Å
Unit-cell length c length_c	51.422 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.77 °
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	1.550 Å
Low-resolution limit resolution_low	37.780 Å
R factor r_factor	0.1726
R_work r_work	0.1712
R_free r_free	0.1993

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand

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

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

5d7c__assembly_2__model_1

5d7c__assembly_2__model_1 | I(q)

5d7c__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand

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

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

5d7c__assembly_2__model_1

5d7c__assembly_2__model_1 | I(q)

5d7c__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)