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1kfv

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

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

Formamido-pyrimidine DNA glycosylase

Lactococcus lactis

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 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3' × 1 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3' × 1 ZINC ION × 1 GLYCEROL × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3' × 1 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3' × 1 ZINC ION × 1 GLYCEROL × 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 3
Chains and sequence ranges Author chain A； PDBConstruct 1–271； UniProt 2–273 Author chain B； PDBConstruct 1–271； 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_id1kfv
Deposition date deposition_date2001-11-23
Structure title titleCrystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.
Keywords keywordsDNA repair enzyme, Abasic site, DNA, N-glycosylase, AP lyase, 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.

1kfv__assembly_1__model_1

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

Download this curve (.dat)

1kfv__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.

1kfv__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）21.26 Å
Rg (electron density)20.39 Å
Total Rg21.22 Å
Atom count2638
Residues285
Excluded volume45956 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1kfv__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1kfv__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 (6)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1kfva1
Class classa — All alpha proteins
Fold Fold folda.156 — S13-like H2TH domain
Superfamily Superfamily superfamilya.156.1 — S13-like H2TH domain
Family Family familya.156.1.2 — Middle domain of MutM-like DNA repair proteins
Domain ID domain_idd1kfva2
Class classb — All beta proteins
Fold Fold foldb.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamilyb.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family familyb.113.1.1 — N-terminal domain of MutM-like DNA repair proteins
Domain ID domain_idd1kfva3
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins
Domain ID domain_idd1kfvb1
Class classa — All alpha proteins
Fold Fold folda.156 — S13-like H2TH domain
Superfamily Superfamily superfamilya.156.1 — S13-like H2TH domain
Family Family familya.156.1.2 — Middle domain of MutM-like DNA repair proteins
Domain ID domain_idd1kfvb2
Class classb — All beta proteins
Fold Fold foldb.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamilyb.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family familyb.113.1.1 — N-terminal domain of MutM-like DNA repair proteins
Domain ID domain_idd1kfvb3
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

CATH v4.4 (4 domains)

Domain ID domain_id1kfvA01
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_id1kfvA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily50 —
Domain ID domain_id1kfvB01
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_id1kfvB02
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)