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4pd2

Crystal structure of a complex between a C248GH LlFpg mutant and a THF containing DNA

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

Formamidopyrimidine-DNA glycosylase

Lactococcus lactis subsp. cremoris

UniProt P42371

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(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3') ; × 1 ;DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') ; × 1 ZINC ION × 1 water × 3 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
1kfv 1kfv 1nnj 1pji 1pjj 1pm5 1tdz 1xc8 2xzf 2xzu 4pcz 4pd2

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name FPG_LACLC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–272； UniProt 2–273

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_id4pd2
Deposition date deposition_date2014-04-17
Structure title titleCrystal structure of a complex between a C248GH LlFpg mutant and a THF containing DNA
Keywords keywordsDNA GLYCOSYLASE, 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.

4pd2__assembly_1__model_1

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

Download this curve (.dat)

4pd2__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.

4pd2__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）21.48 Å
Rg (electron density)20.53 Å
Total Rg21.38 Å
Atom count2707
Residues299
Excluded volume46864 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4pd2__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 (5)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4pd2A01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily10 — MutM-like, N-terminal
Domain ID domain_id4pd2A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily50 —
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7. Citations (1)