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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 298–384	Fragment：Homeobox DNA-binding domain	;DNA (5'-D(DAPDCPDTPDCPDTPDAPDTPDGPDAPDTPDTPDTPDAPDTPDGPDGPDGPDCPDTPDG)-3') ; × 1 ;DNA (5'-D(DTPDCPDAPDGPDCPDCPDCPDAPDTPDAPDAPDAPDTPDCPDAPDTPDAPDGPDAPDG)-3') ; × 1 Homeobox protein extradenticle × 1 （P40427）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.7；277 K；20% MPD, 10-14% PEG 4000, 0.2M sodium acetate, 0.2M potassium chloride, 0.1M Tris , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2R5Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2R5Z Structure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene Deposited 2007-09-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 298–384（87 aa） Fragment：Homeobox DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.7；10-14 % PEG 4K, 20 % MPD, 0.1 M Tris, pH 8.7-8.9, 0.2 M Sodium Acetate, 0.2 M Potassium Chloride	Resolution 2.60 Å R-free 0.303

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 238–300	Fragment：Homeobox TALE-type DNA-binding domain	;DNA (5'-D(DAPDCPDTPDCPDTPDAPDTPDGPDAPDTPDTPDTPDAPDTPDGPDGPDGPDCPDTPDG)-3') ; × 1 ;DNA (5'-D(DTPDCPDAPDGPDCPDCPDCPDAPDTPDAPDAPDAPDTPDCPDAPDTPDAPDGPDAPDG)-3') ; × 1 Homeotic protein Sex combs reduced × 1 （P09077）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.7；277 K；20% MPD, 10-14% PEG 4000, 0.2M sodium acetate, 0.2M potassium chloride, 0.1M Tris , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2R5Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8I STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX Deposited 1999-02-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–300（63 aa） Fragment：HOMEODOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；0.6M AMMONIUM PHOSPHATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.304
2R5Z Structure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene Deposited 2007-09-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–300（63 aa） Fragment：Homeobox TALE-type DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.7；10-14 % PEG 4K, 20 % MPD, 0.1 M Tris, pH 8.7-8.9, 0.2 M Sodium Acetate, 0.2 M Potassium Chloride	Resolution 2.60 Å R-free 0.303
4CYC CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS Deposited 2014-04-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–312（75 aa） Fragment：HOMEODOMAIN RESIDUES 238-312	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M AMMONIUM PHOSPHATE, pH 7.5	Resolution 2.36 Å R-free 0.227
4UUS CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF Deposited 2014-07-31	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–312（75 aa） Fragment：HOMEODOMAIN RESIDUES 238-312	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000	Resolution 2.55 Å R-free 0.239
4UUS CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF Deposited 2014-07-31	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain F 238–312（75 aa） Fragment：HOMEODOMAIN RESIDUES 238-312	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000	Resolution 2.55 Å R-free 0.239
5ZJQ Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence Deposited 2018-03-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 4000, 5% glycerol	Resolution 2.44 Å R-free 0.252
5ZJR Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence Deposited 2018-03-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；90mM MgCl2, 0.1M Tris pH9.0, 22% PEG 3350	Resolution 3.03 Å R-free 0.288
5ZJS Structure of AbdB/Exd complex bound to a 'Blue14' DNA sequence Deposited 2018-03-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 3350, 2.5% glycerol	Resolution 2.90 Å R-free 0.281
5ZJT Structure of AbdB/Exd complex bound to a 'Black14' DNA sequence Deposited 2018-03-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Sodium citrate pH 5.3, 25% PEG 3350	Resolution 2.40 Å R-free 0.276
7YB4 Solution structure of homeodomain of EXTRADENTICLE Deposited 2022-06-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 238–300（63 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.6 mM [U-13C; U-15N] Homeobox protein Extradenticle, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-13C; U-15N] Homeobox protein Extradenticle, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.46 Å
Radius of gyration Rg (electron density) rg_electron	19.83 Å
Forward intensity I(0) i0	22872600.00
Molecular weight molecular_weight	28513.0 kDa
Excluded volume excluded_volume	32272 Å³
Envelope volume envelope_volume	42035 Å³
Hydration-shell volume shell_volume	18375 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	25.52 Å
Envelope Rg envelope_rg	20.02 Å
Shape Rg shape_rg	19.80 Å
Total Rg total_rg	20.57 Å
Total atoms total_atoms	1963
Residues n_residues	172
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.9 Å
Rg (real space) rg_real	20.48 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	2.2870e+07
I(0) uncertainty (real space) i0_real_error	3.2600e+05
Rg (reciprocal space) rg_reciprocal	20.48 Å
I(0) (reciprocal space) i0_reciprocal	22870000.0000
Solution quality estimate total_estimate	0.7819
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.151
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3367000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.737; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 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

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/r5/2r5y/2r5y.fit
pddf	/app/data/pr_computation/r5/2r5y/2r5y.pr.out
profile	/app/data/saxs_computation/r5/2r5y/2r5y.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. 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

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)