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5zjt

Structure of AbdB/Exd complex bound to a 'Black14' DNA sequence

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

Homeobox protein abdominal-B

Drosophila melanogaster

UniProt P09087

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 Homeobox protein extradenticle × 1 （P40427） ;DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3') ; × 1 water × 4 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3') ; × 1 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
5zjq 5zjr 5zjs 5zjt 5zjt

5 assemblies

View Construct and Data Evidence
UniProt name ABDB_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–84； UniProt 369–452 Author chain E； PDBConstruct 1–84； UniProt 369–452

Homeobox protein extradenticle

Drosophila melanogaster

UniProt P40427

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 Homeobox protein abdominal-B × 1 （P09087） ;DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3') ; × 1 ;DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3') ; × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
7yb4

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1b8i 2r5y 2r5z 4cyc 4uus 4uus 5zjq 5zjr 5zjs 5zjt

10 assemblies

View Construct and Data Evidence
UniProt name EXD_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–74； UniProt 237–310

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_id5zjt
Deposition date deposition_date2018-03-22
Structure title titleStructure of AbdB/Exd complex bound to a 'Black14' DNA sequence
Keywords keywordsAbdB, Exd, DNA, shape, specificity, Hox, Homeodomain, TRANSCRIPTION, 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.

5zjt__assembly_1__model_1

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

Download this curve (.dat)

5zjt__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.

5zjt__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）18.39 Å
Rg (electron density)18.23 Å
Total Rg18.89 Å
Atom count1695
Residues163
Excluded volume28249 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5zjt__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5zjt__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 (5)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id5zjtA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5zjtB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5zjtE00
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)