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6x9j

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

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

DNA (cytosine-5)-methyltransferase 1

Homo sapiens

UniProt P26358

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(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(*GP*CP*AP*GP*G)-R(P*(PYO))-D(P*GP*GP*CP*CP*TP*C)-3') ; × 1 ZINC ION × 2 1,2-ETHANEDIOL × 17 N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
3epz 3epz 3swr 4wxx 4wxx 8v9u

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3pta 4yoc 4z96 5wvo 5ydr 6l1f 6x9i 6x9j 6x9k 7sfc 7sfd 7sfe

21 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DNMT1_HUMAN
Isoform P26358-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–874； UniProt 393–1264

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_id6x9j
Deposition date deposition_date2020-06-02
Structure title titleHuman DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052
Keywords keywords;EPIGENETICS, DNA METHYLTRANSFERASE FOLD, MAINTENANCE METHYLATION, INHIBITION, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex, TRANSFERASE-TRANSFERASE INHIBITOR-DNA complex ;; TRANSFERASE/TRANSFERASE INHIBITOR/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.

6x9j__assembly_1__model_1

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

Download this curve (.dat)

6x9j__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.

6x9j__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）31.74 Å
Rg (electron density)31.04 Å
Total Rg31.54 Å
Atom count7071
Residues864
Excluded volume123590 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6x9j__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 (7)

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6x9jA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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7. Citations (1)