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3pt6

Crystal structure of mouse DNMT1(650-1602) in complex with DNA

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

DNA (cytosine-5)-methyltransferase 1

Mus musculus

UniProt P13864

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(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') ; × 1 ;DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 ZINC ION × 4 water × 1 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') ; × 1 ;DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 ZINC ION × 4 water × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
3av4 3av5 3av6 3pt9 5gut 5guv

6 assemblies

Homodimer
5wy1

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3pt6 3pt6 4da4 4da4 6w8v 6w8w

6 assemblies

View Construct and Data Evidence
UniProt name DNMT1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–954； UniProt 650–1602 Author chain B； PDBConstruct 2–954； UniProt 650–1602

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_id3pt6
Deposition date deposition_date2010-12-02
Structure title titleCrystal structure of mouse DNMT1(650-1602) in complex with DNA
Keywords keywordsMaintenance DNA methylation, Transferase-DNA complex; Transferase/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.

3pt6__assembly_1__model_1

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

Download this curve (.dat)

3pt6__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.

3pt6__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）33.70 Å
Rg (electron density)32.84 Å
Total Rg33.39 Å
Atom count7773
Residues952
Excluded volume134270 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3pt6__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3pt6__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 (10 domains)

Domain ID domain_idd3pt6a1
Class classg — Small proteins
Fold Fold foldg.95 — bi-CXXC zinc finger-like
Superfamily Superfamily superfamilyg.95.1 — bi-CXXC zinc finger-like
Family Family familyg.95.1.1 — bi-CXXC zinc finger-like
Domain ID domain_idd3pt6a2
Class classj — Peptides
Fold Fold foldj.129 — DNMT1 CXXC-BAH1 linker domain-like
Superfamily Superfamily superfamilyj.129.1 — DNMT1 CXXC-BAH1 linker domain-like
Family Family familyj.129.1.1 — DNMT1 CXXC-BAH1 linker domain-like
Domain ID domain_idd3pt6a3
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.12 — BAH domain
Family Family familyb.34.12.1 — BAH domain
Domain ID domain_idd3pt6a4
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.12 — BAH domain
Family Family familyb.34.12.1 — BAH domain
Domain ID domain_idd3pt6a5
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.26 — C5 cytosine-specific DNA methylase, DCM
Domain ID domain_idd3pt6b1
Class classg — Small proteins
Fold Fold foldg.95 — bi-CXXC zinc finger-like
Superfamily Superfamily superfamilyg.95.1 — bi-CXXC zinc finger-like
Family Family familyg.95.1.1 — bi-CXXC zinc finger-like
Domain ID domain_idd3pt6b2
Class classj — Peptides
Fold Fold foldj.129 — DNMT1 CXXC-BAH1 linker domain-like
Superfamily Superfamily superfamilyj.129.1 — DNMT1 CXXC-BAH1 linker domain-like
Family Family familyj.129.1.1 — DNMT1 CXXC-BAH1 linker domain-like
Domain ID domain_idd3pt6b3
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.12 — BAH domain
Family Family familyb.34.12.1 — BAH domain
Domain ID domain_idd3pt6b4
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.12 — BAH domain
Family Family familyb.34.12.1 — BAH domain
Domain ID domain_idd3pt6b5
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.26 — C5 cytosine-specific DNA methylase, DCM
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7. Citations (1)