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3ogd

AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair

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

DNA-3-methyladenine glycosylase 2

Escherichia coli

UniProt P04395

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 5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3' × 1 5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3' × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1mpg 1mpg 1pvs 1pvs

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1diz 1diz 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu 3d4v 3ogd 3oh6

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name 3MG2_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–289； UniProt 2–282

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_id3ogd
Deposition date deposition_date2010-08-16
Structure title titleAlkA Undamaged DNA Complex: Interrogation of a G*:C base pair
Keywords keywordshelix-hairpin-helix, DNA repair, Alkylation, HYDROLASE-DNA complex; HYDROLASE/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.

3ogd__assembly_1__model_1

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

Download this curve (.dat)

3ogd__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3ogd__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）21.72 Å
Rg (electron density)20.32 Å
Total Rg21.24 Å
Atom count2621
Residues304
Excluded volume45636 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ogd__assembly_1__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 (3)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3ogdA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain
Domain ID domain_id3ogdA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3ogdA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
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7. Citations (1)