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5cdm

2.5A structure of QPT-1 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 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(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 MANGANESE (II) ION × 2 GLYCEROL × 2 SULFATE ION × 1 SODIUM ION × 1 ;(2R,4S,4aS)-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4',6'(1'H,3'H)-trione ; × 2 THYMIDINE-5'-MONOPHOSPHATE × 1 water × 8 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 1
Chains and sequence ranges Author chain B； PDBConstruct 1–128； UniProt 416–543 Author chain B； PDBConstruct 131–190； UniProt 580–639 Author chain D； PDBConstruct 1–128； UniProt 416–543 Author chain D； PDBConstruct 131–190； UniProt 580–639

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 Protein–DNA Heteromer Protein 4 DNA 4 DNA gyrase subunit B,DNA gyrase subunit B × 2 （P66937） ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 ;DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') ; × 2 MANGANESE (II) ION × 2 GLYCEROL × 2 SULFATE ION × 1 SODIUM ION × 1 ;(2R,4S,4aS)-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4',6'(1'H,3'H)-trione ; × 2 THYMIDINE-5'-MONOPHOSPHATE × 1 water × 8 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 2
Chains and sequence ranges Author chain A； PDBConstruct 1–482； UniProt 9–490 Author chain C； PDBConstruct 1–482； UniProt 9–490

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_id5cdm
Deposition date deposition_date2015-07-04
Structure title title2.5A structure of QPT-1 with S.aureus DNA gyrase and DNA
Keywords keywordsTYPE IIA TOPOISOMERASE, ANTIBACTERIAL, INHIBITOR, 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.

5cdm__assembly_1__model_1

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

Download this curve (.dat)

5cdm__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.

5cdm__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）37.23 Å
Rg (electron density)37.02 Å
Total Rg37.39 Å
Atom count22442
Residues1378
Excluded volume199840 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5cdm__assembly_1__model_1 octameric （8） 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 (11)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5cdmB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id5cdmD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
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7. Citations (2)