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1m0e

ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE

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

Modification methylase HhaI

Haemophilus haemolyticus

UniProt P05102

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(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3' × 1 5'-D(P*GP*TP*CP*AP*GP*(Z)P*GP*CP*AP*TP*GP*G)-3' × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1hmy 1svu 1svu 2hmy

4 assemblies

Homodimer
5lod

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
10mh 1fjx 1m0e 1mht 1skm 2c7o 2c7p 2c7q 2c7r 2hr1 2i9k 2uyc

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name MTH1_HAEHA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–327； UniProt 1–327

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_id1m0e
Deposition date deposition_date2002-06-12
Structure title titleZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE
Keywords keywordsProtein-DNA covalent complex, Mechanism based DNA methylation inhibitors, Zebularine, 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.

1m0e__assembly_1__model_1

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

Download this curve (.dat)

1m0e__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.

1m0e__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）21.65 Å
Rg (electron density)20.63 Å
Total Rg21.49 Å
Atom count3134
Residues350
Excluded volume53669 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1m0e__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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1m0ea_
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

CATH v4.4 (2 domains)

Domain ID domain_id1m0eA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id1m0eA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology120 — DNA Methylase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Methylase, subunit A, domain 2
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7. Citations (1)