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6cnq

MBD2 in complex with methylated DNA

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

Methyl-CpG-binding domain protein 2

Homo sapiens

UniProt Q9UBB5

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*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3') ; × 2 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3') ; × 2 UNKNOWN ATOM OR ION × 4 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
2l2l 6c1a 6c1a 6c1t 6c1u 6c1u 6c1v 6c1v 6c2f 6c2f 6c2f 6c2f

26 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name MBD2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–79； UniProt 143–220 Author chain B； PDBConstruct 2–79； UniProt 143–220

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_id6cnq
Deposition date deposition_date2018-03-08
Structure title titleMBD2 in complex with methylated DNA
Keywords keywordsdna methylation, dna binding, Structural Genomics, Structural Genomics Consortium, SGC, TRANSCRIPTION-DNA complex; TRANSCRIPTION/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.

6cnq__assembly_1__model_1

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

Download this curve (.dat)

6cnq__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6cnq__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）15.84 Å
Rg (electron density)15.08 Å
Total Rg15.99 Å
Atom count1003
Residues90
Excluded volume16305 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6cnq__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6cnq__assembly_2__model_1 trimeric （3） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6cnqA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology890 — Methyl-cpg-binding Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Methyl-cpg-binding Protein 2; Chain A
Domain ID domain_id6cnqB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology890 — Methyl-cpg-binding Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Methyl-cpg-binding Protein 2; Chain A
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7. Citations (1)