SAXSdb — 5zjr

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Homeobox protein abdominal-B

Drosophila melanogaster

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(GPTPCPGPTPAPAPAPTPCPAPTPGPC)-3') ; × 1 ;DNA (5'-D(PGPCPAPTPGPAPTPTPTPAPCPGPAPC)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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

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(GPTPCPGPTPAPAPAPTPCPAPTPGPC)-3') ; × 1 ;DNA (5'-D(PGPCPAPTPGPAPTPTPTPAPCPGPAPC)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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_id	5zjr
Deposition date deposition_date	2018-03-22
Structure title title	Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence
Keywords keywords	AbdB, Exd, DNA, shape, specificity, Hox, Homeodomain, TRANSCRIPTION, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
Experimental Method method	X-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.

5zjr__assembly_1__model_1

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

Download this curve (.dat)

5zjr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zjr__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.29 Å
Rg (electron density)	18.14 Å
Total Rg	18.86 Å
Atom count	1660
Residues	166
Excluded volume	27603 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zjr__assembly_1__model_1`	tetrameric （4）	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)

Entity 1 Entity 1 polymer

Description description	Homeobox protein abdominal-B
Molecular weight formula_weight	10195.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1660

VGPCTPNPGLHEWTGQVSVRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRRMKNKKNSQRQANQ

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Homeobox protein extradenticle
Molecular weight formula_weight	8773.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLY

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPTPCPGPTPAPAPAPTPCPAPTPGPC)-3') ;
Molecular weight formula_weight	4279.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GTCGTAAATCATGC

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PGPCPAPTPGPAPTPTPTPAPCPGPAPC)-3') ;
Molecular weight formula_weight	4279.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GCATGATTTACGAC

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5zjrA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	5zjrB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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Unit-cell length a length_a	77.330 Å
Unit-cell length b length_b	49.445 Å
Unit-cell length c length_c	95.092 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.030 Å
Low-resolution limit resolution_low	44.906 Å
R factor r_factor	0.2697
R_work r_work	0.2687
R_free r_free	0.2880

Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence

1. Protein Identity and Related Structures Protein Identity & Related Structures

Homeobox protein abdominal-B

State in the Current Structure

Other States of the Same Protein in the Database

Homeobox protein extradenticle

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5zjr__assembly_1__model_1

5zjr__assembly_1__model_1 | I(q)

5zjr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence

1. Protein Identity and Related Structures Protein Identity & Related Structures

Homeobox protein abdominal-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Homeobox protein extradenticle

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5zjr__assembly_1__model_1

5zjr__assembly_1__model_1 | I(q)

5zjr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)