SAXSdb — 2r5y

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

Homeotic protein Sex combs reduced

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	;DNA (5'-D(DAPDCPDTPDCPDTPDAPDTPDGPDAPDTPDTPDTPDAPDTPDGPDGPDGPDCPDTPDG)-3') ; × 1 ;DNA (5'-D(DTPDCPDAPDGPDCPDCPDCPDAPDTPDAPDAPDAPDTPDCPDAPDTPDAPDGPDAPDG)-3') ; × 1 Homeobox protein extradenticle × 1 （P40427） water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCR_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 2–88； UniProt 298–384

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	;DNA (5'-D(DAPDCPDTPDCPDTPDAPDTPDGPDAPDTPDTPDTPDAPDTPDGPDGPDGPDCPDTPDG)-3') ; × 1 ;DNA (5'-D(DTPDCPDAPDGPDCPDCPDCPDAPDTPDAPDAPDAPDTPDCPDAPDTPDAPDGPDAPDG)-3') ; × 1 Homeotic protein Sex combs reduced × 1 （P09077） water × 4	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	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–63； UniProt 238–300

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	2r5y
Deposition date deposition_date	2007-09-04
Structure title title	Structure of Scr/Exd complex bound to a consensus Hox-Exd site
Keywords keywords	;Homeodomain, homeotic proteins, specificity, Developmental protein, DNA-binding, Homeobox, Nucleus, Transcription, Transcription regulation, 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.

2r5y__assembly_1__model_1

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

Download this curve (.dat)

2r5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.46 Å
Rg (electron density)	19.83 Å
Total Rg	20.57 Å
Atom count	1963
Residues	172
Excluded volume	32272 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5y__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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DAPDCPDTPDCPDTPDAPDTPDGPDAPDTPDTPDTPDAPDTPDGPDGPDGPDCPDTPDG)-3') ;
Molecular weight formula_weight	6155.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2066

ACTCTATGATTTATGGGCTG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DTPDCPDAPDGPDCPDCPDCPDAPDTPDAPDAPDAPDTPDCPDAPDTPDAPDGPDAPDG)-3') ;
Molecular weight formula_weight	6111.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TCAGCCCATAAATCATAGAG

Entity 3 Entity 3 polymer

Description description	Homeotic protein Sex combs reduced
Molecular weight formula_weight	10967.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GKKNPPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK

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 4 Entity 4 polymer

Description description	Homeobox protein extradenticle
Molecular weight formula_weight	7553.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNI

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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2r5ya1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

Domain ID domain_id	d2r5ya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2r5yb_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

CATH v4.4 (2 domains)

Domain ID domain_id	2r5yA00
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	2r5yB00
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	65.310 Å
Unit-cell length b length_b	65.310 Å
Unit-cell length c length_c	200.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	11.960 Å
R factor r_factor	0.2550
R_work r_work	0.2550
R_free r_free	0.2990

Structure of Scr/Exd complex bound to a consensus Hox-Exd site

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

Homeotic protein Sex combs reduced

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

2r5y__assembly_1__model_1

2r5y__assembly_1__model_1 | I(q)

2r5y__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Scr/Exd complex bound to a consensus Hox-Exd site

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

Homeotic protein Sex combs reduced

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

2r5y__assembly_1__model_1

2r5y__assembly_1__model_1 | I(q)

2r5y__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)