SAXSdb — 1s5r

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

high mobility group box transcription factor 1

OrganismNot specified

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 358–380	Fragment：Sin3 Interaction Domain, Residues 6 to 21	Sin3a protein × 1 （Q60520）	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6, 0.2% NaN3；Pressure ambient NMR sample composition：1.1 mM 1:1 SID UNLABELED, PAH2 U-15N \| 90% H2O/10% D2O NMR sample composition：1.4 mM 1:1 SID UNLABELED, PAH2 U-15N,13C \| 100% D2O	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8BUS3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–23； UniProt 358–380

Sin3a protein

Mus musculus

UniProt Q60520

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 295–383	Fragment：Paired Amphipathic Helix 2, (PAH2 repeat), Residues 295 to 383	high mobility group box transcription factor 1 × 1 （Q8BUS3）	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6, 0.2% NaN3；Pressure ambient NMR sample composition：1.1 mM 1:1 SID UNLABELED, PAH2 U-15N \| 90% H2O/10% D2O NMR sample composition：1.4 mM 1:1 SID UNLABELED, PAH2 U-15N,13C \| 100% D2O	Resolution not provided

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 1S5R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G1E NMR STRUCTURE OF THE HUMAN MAD1 TRANSREPRESSION DOMAIN SID IN COMPLEX WITH MAMMALIAN SIN3A PAH2 DOMAIN Deposited 2000-10-11	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–383（89 aa） Fragment：PAIRED AMPHIPATHIC HELIX 2 (PAH2 REPEAT)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR sample composition 1.0 mM 1:1 SID unlabeled, PAH2 U-15N; 1.6 mM 1:1 SID unlabeled, PAH2 U-15N, U-13C. \| 90% H2O/10% D2O NMR sample composition 1.6 mM 1:1 SID unlabeled, PAH2 U-15N,13C; 20 mM phosphate buffer pH 6.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1.6 mM 1:1 SID unlabeled, PAH2 U-15N,13C; 20 mM phosphate buffer pH 6.0, 0.2% NaN3 \| 100% D2O	Resolution not provided
1S5Q Solution Structure of Mad1 SID-mSin3A PAH2 Complex Deposited 2004-01-21	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–383（89 aa） Fragment：Paired Amphipathic Helix 2, (PAH2 repeat), Residues 295 to 383	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6, 0.2% NaN3；Pressure ambient NMR sample composition 1.0 mM 1:1 SID UNLABELED, PAH2 U-15N \| 90% H2O/10% D2O NMR sample composition 1.6 mM 1:1 SID UNLABELED, PAH2 U-15N,U-13C \| 100% D2O	Resolution not provided
2L9S Solution structure of Pf1 SID1-mSin3A PAH2 Complex Deposited 2011-02-23	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–385（91 aa） Fragment：PAH 2 domain residues 295-385	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.75-1.5 mM [U-100% 13C; U-100% 15N] peptide, 0.75-1.5 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LD7 Solution structure of the mSin3A PAH3-SAP30 SID complex Deposited 2011-05-16	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 456–528（73 aa） Fragment：PAH 3 domain residues 456-528	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein 1, 1 mM protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM protein 1, 1 mM [U-100% 13C; U-100% 15N] protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein 1, 1 mM protein 2, 100% D2O \| 100% D2O NMR sample composition 1 mM protein 1, 1 mM [U-100% 13C; U-100% 15N] protein 2, 100% D2O \| 100% D2O	Resolution not provided
2N2H Solution structure of Sds3 in complex with Sin3A Deposited 2015-05-08	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 608–729（122 aa） Fragment：UNP residues 608-729	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；303 K；Ionic strength (raw mmCIF value) 0.12；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] Sin3HID, 0.5-1 mM Sds3SID, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] Sds3SID, 0.5-1 mM Sin3HID, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RMR Solution structure of mSin3A PAH1 domain Deposited 2007-11-14	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 119–189（71 aa） Fragment：UNP residues 119-189	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) .02；Pressure ambient NMR sample composition 0.7-1.0mM [U-13C; U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.7-1.0mM [U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0mM [U-13C; U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RMS Solution structure of the mSin3A PAH1-SAP25 SID complex Deposited 2007-11-14	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 119–189（71 aa） Fragment：UNP residues 119-189	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) .02；Pressure ambient NMR sample composition 0.7-1.0mM [U-15N] SIN3A, 0.7-1.0mM SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0mM SIN3A, 0.7-1.0mM [U-15N] SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0mM [U-13C; U-15N] SIN3A, 0.7-1.0mM SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.7-1.0mM SIN3A , 0.7-1.0mM [U-13C; U-15N] SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O \| 100% D2O	Resolution not provided

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SIN3A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–89； UniProt 295–383

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	1s5r
Deposition date deposition_date	2004-01-21
Structure title title	Solution Structure of HBP1 SID-mSin3A PAH2 Complex
Keywords keywords	Protein-peptide complex, Amphipathic helix motif, Four-helix bundle, Repressor-corepressor complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.29 Å
Radius of gyration Rg (electron density) rg_electron	14.57 Å
Forward intensity I(0) i0	969466000.00
Molecular weight molecular_weight	258150.0 kDa
Excluded volume excluded_volume	320450 Å³
Envelope volume envelope_volume	38378 Å³
Hydration-shell volume shell_volume	17916 Å³
Envelope diameter envelope_diameter	61.3 Å
Shell Rg shell_rg	24.33 Å
Envelope Rg envelope_rg	18.70 Å
Shape Rg shape_rg	14.54 Å
Total Rg total_rg	14.86 Å
Total atoms total_atoms	35900
Residues n_residues	2240
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	54.4 Å
Rg (real space) rg_real	15.23 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	9.6950e+08
I(0) uncertainty (real space) i0_real_error	1.0030e+07
Rg (reciprocal space) rg_reciprocal	15.24 Å
I(0) (reciprocal space) i0_reciprocal	969500000.0000
Solution quality estimate total_estimate	0.7591
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.239
Kurtosis Kurtosis kurtosis	-0.201
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	327300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.627; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1s5ra_
Class class	j — Peptides
Fold Fold fold	j.114 — HMG-box transcription factor 1 fragments
Superfamily Superfamily superfamily	j.114.1 — HMG-box transcription factor 1 fragments
Family Family family	j.114.1.1 — HMG-box transcription factor 1 fragments

Domain ID domain_id	d1s5rb_
Class class	a — All alpha proteins
Fold Fold fold	a.59 — PAH2 domain
Superfamily Superfamily superfamily	a.59.1 — PAH2 domain
Family Family family	a.59.1.1 — PAH2 domain

CATH v4.4 (1 domains)

Domain ID domain_id	1s5rB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1160 — Paired amphipathic helix 2 (pah2 repeat)
Homologous superfamily homologous superfamily	11 — Paired amphipathic helix

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	high mobility group box transcription factor 1
Molecular weight formula_weight	2578.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	35900

Description description	Sin3a protein
Molecular weight formula_weight	10343.4 kDa
Source method src_method	man
Copy count entity_count	1

Solution Structure of HBP1 SID-mSin3A PAH2 Complex

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

high mobility group box transcription factor 1

State in the Current Structure

Other States of the Same Protein in the Database

Sin3a protein

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/s5/1s5r/1s5r.fit
pddf	/app/data/pr_computation/s5/1s5r/1s5r.pr.out
profile	/app/data/saxs_computation/s5/1s5r/1s5r.dat