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6w4t

APE1 Y269A phosphorothioate substrate complex with abasic DNA

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

DNA-(apurinic or apyrimidinic site) lyase

Homo sapiens

UniProt P27695

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') ; × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') ; × 1 water × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1bix 1e9n 1e9n 1hd7 2isi 2isi 2isi 2o3h 3u8u 3u8u 3u8u 3u8u

65 assemblies; showing the first 12

Homodimer
7mcr

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1cqg 1cqh 1de8 1de8 1de9 1de9 1dew 1dew 4iem 4iem 4iem 4iem

58 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name APEX1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–276； UniProt 43–318 Author chain B； PDBConstruct 1–276； UniProt 43–318

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_id6w4t
Deposition date deposition_date2020-03-11
Structure title titleAPE1 Y269A phosphorothioate substrate complex with abasic DNA
Keywords keywordsDNA Repair, AP-Endonuclease, DNA Binding, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex, LYASE-DNA complex; LYASE/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.

6w4t__assembly_1__model_1

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

Download this curve (.dat)

6w4t__assembly_1__model_1 | I(q)

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

6w4t__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）23.38 Å
Rg (electron density)21.88 Å
Total Rg22.83 Å
Atom count3038
Residues317
Excluded volume51310 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6w4t__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6w4t__assembly_2__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6w4tA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily10 — Endonuclease/exonuclease/phosphatase
Domain ID domain_id6w4tB00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily10 — Endonuclease/exonuclease/phosphatase
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7. Citations (1)