← Back to search
5cdq

2.95A structure of Moxifloxacin 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 (strain N315)

UniProt Q99XG5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 2 （P66937） ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 MAGNESIUM ION × 7 GLYCEROL × 4 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid × 3 water × 6 Consistent with all polymers
2 Protein–DNA Heteromer Protein 4 DNA 2 DNA gyrase subunit B,DNA gyrase subunit B × 2 （P66937） ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 MAGNESIUM ION × 7 GLYCEROL × 4 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid × 3 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2xco 2xcq 2xcr 2xcr 2xcs 2xct 2xct 4bul 5cdm 5cdn 5cdn 5cdo

41 assemblies; showing the first 12

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 2 DNA gyrase subunit A × 2 （Q99XG5） ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 MAGNESIUM ION × 7 GLYCEROL × 4 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid × 3 water × 6 Consistent with all polymers
2 Protein–DNA Heteromer Protein 4 DNA 2 DNA gyrase subunit A × 2 （Q99XG5） ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 MAGNESIUM ION × 7 GLYCEROL × 4 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid × 3 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2xco 2xcq 2xcr 2xcr 2xcs 2xct 2xct 4bul 5cdm 5cdn 5cdn 5cdo

38 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name GYRB_STAAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–193； UniProt 414–640 Author chain D； PDBConstruct 1–193； UniProt 414–640 Author chain S； PDBConstruct 1–193； UniProt 414–640 Author chain U； PDBConstruct 1–193； UniProt 414–640

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_id5cdq
Deposition date deposition_date2015-07-04
Structure title title2.95A structure of Moxifloxacin with S.aureus DNA gyrase and DNA
Keywords keywordsTYPE IIA TOPOISOMERASE, ANTIBACTERIAL, INHIBITOR, hydrolase; HYDROLASE
Experimental Method methodX-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.

5cdq__assembly_2__model_1

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

Download this curve (.dat)

5cdq__assembly_2__model_1 | I(q)

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

5cdq__assembly_2__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）37.17 Å
Rg (electron density)36.95 Å
Total Rg37.31 Å
Atom count11380
Residues1385
Excluded volume199490 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5cdq__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5cdq__assembly_2__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5cdqB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id5cdqD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id5cdqS01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id5cdqU01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
▶

7. Citations (2)