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5ef6

Structure of HOXB13 complex with methylated DNA

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

Homeobox protein Hox-B13

Homo sapiens

UniProt Q92826

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(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') ; × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') ; × 1 water × 3 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') ; × 1 water × 3 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') ; × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2cra

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5edn 5edn 5edn 5edn 5eea 5eea 5eea 5eea 5ef6 5ef6 5ef6 5ef6

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HXB13_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–62； UniProt 217–278 Author chain B； PDBConstruct 1–62； UniProt 217–278 Author chain G； PDBConstruct 1–62； UniProt 217–278 Author chain J； PDBConstruct 1–62； UniProt 217–278

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_id5ef6
Deposition date deposition_date2015-10-23
Structure title titleStructure of HOXB13 complex with methylated DNA
Keywords keywordstranscription factor, methylated DNA, complex, transcription; TRANSCRIPTION
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.

5ef6__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ef6__assembly_3__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5ef6__assembly_3__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）18.33 Å
Rg (electron density)17.37 Å
Total Rg18.21 Å
Atom count1268
Residues96
Excluded volume20361 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5ef6__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5ef6__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5ef6__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5ef6__assembly_4__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 (4)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5ef6A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5ef6B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5ef6G00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5ef6J00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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7. Citations (1)