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4fm9

Human topoisomerase II alpha bound to DNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA topoisomerase 2-alpha

Homo sapiens

UniProt P11388

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 4 ;DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3') ; × 2 ;DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3') ; × 2 MAGNESIUM ION × 4 GLYCEROL × 2 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1zxm 1zxn 1zxn 4r1f 4r1f 8w50 8w50 9bq6 9bq7 9bq9 9bqb

11 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4fm9 5gwk 6zy5 6zy6 6zy7 6zy8

6 assemblies

View Construct and Data Evidence
UniProt name TOP2A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–763； UniProt 431–1193

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_id4fm9
Deposition date deposition_date2012-06-15
Structure title titleHuman topoisomerase II alpha bound to DNA
Keywords keywordsTOPOISOMERASE, DNA-BINDING, PROTEIN-DNA COMPLEX, ISOMERASE-DNA COMPLEX; ISOMERASE/DNA
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.

4fm9__assembly_1__model_1

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

Download this curve (.dat)

4fm9__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.

4fm9__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）37.77 Å
Rg (electron density)37.50 Å
Total Rg38.01 Å
Atom count13076
Residues1514
Excluded volume230230 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4fm9__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 (6)

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id4fm9A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id4fm9A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id4fm9A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
Domain ID domain_id4fm9A04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4fm9A05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
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7. Citations (1)