SAXSdb — 1z87

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

Alpha-1-syntrophin

Mus musculus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–264	Fragment：the PHN-PDZ-PHC tandem	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；303 K；Pressure ambient NMR sample composition：1mM PHN-PDZ-PHC tandem of alpha1-syntrophin U-15N, 13C; 100mM potassium phosphate; 90% H2O,10% D2O \| 90% H2O/10% D2O NMR sample composition：1mM PHN-PDZ-PHC tandem of alpha1-syntrophin U-15N; 100mM potassium phosphate; 90% H2O,10% D2O \| 90% H2O/10% D2O NMR sample composition：1mM PHN-PDZ-PHC tandem of alpha1-syntrophin U-15N, 13C; 100mM potassium phosphate; 99.9% D2O \| 99.9% D2O NMR sample composition：1mM PHN-PDZ-PHC tandem of alpha1-syntrophin; 100mM potassium phosphate; 99.9% D2O \| 99.9% 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 1Z87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QAV Unexpected Modes of PDZ Domain Scaffolding Revealed by Structure of NNOS-Syntrophin Complex Deposited 1999-03-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 75–164（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；VAPOR DIFFUSION, SITTING DROP, PH 8.5, 298K, 25% PEG4000, 0.2M SODIUM ACETATE, 100MM TRIS	Resolution 1.90 Å R-free 0.259
1Z86 Solution structure of the PDZ domain of alpha-syntrophin Deposited 2005-03-30	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–165（87 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Pressure ambient NMR sample composition 1mM PDZ domain of alpha1-syntrophin U-15N, 13C; 100mM potassium phosphate; 90% H2O,10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM PDZ domain of alpha1-syntrophin U-15N; 100mM potassium phosphate; 90% H2O,10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM PDZ domain of alpha1-syntrophin U-15N, 13C; 100mM potassium phosphate; 99.9% D2O \| 99.9% D2O NMR sample composition 1mM PDZ domain of alpha1-syntrophin; 100mM potassium phosphate; 99.9% D2O \| 99.9% D2O	Resolution not provided
2ADZ solution structure of the joined PH domain of alpha1-syntrophin Deposited 2005-07-21	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–79（78 aa） Fragment：PH domain Chain A 165–264（100 aa） Fragment：PH domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Pressure ambient NMR sample composition 1mM protein 15N; 100mM potassium phosphate pH 7.0 \| 90% H2O/10% D2O NMR sample composition 1mM protein 15N, 13C; 100mM potassium phosphate pH 7.0 \| 99.9% D2O NMR sample composition 1mM unlabelled protein; 100mM potassium phosphate pH 7.0 \| 99.9% D2O	Resolution not provided
2PDZ SOLUTION STRUCTURE OF THE SYNTROPHIN PDZ DOMAIN IN COMPLEX WITH THE PEPTIDE GVKESLV, NMR, 15 STRUCTURES Deposited 1997-12-10	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 79–164（86 aa） Fragment：PDZ DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；295 K；Ionic strength (raw mmCIF value) 70mM；Pressure 1 NMR sample composition H2O	Resolution not provided
4HOP Crystal structure of the computationally designed NNOS-Syntrophin complex Deposited 2012-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–162（86 aa） Fragment：PDZ DOMAIN (RESIDUES 77-162)	Mutation：H142F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；293 K；0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.29 Å R-free 0.273
4HOP Crystal structure of the computationally designed NNOS-Syntrophin complex Deposited 2012-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 77–162（86 aa） Fragment：PDZ DOMAIN (RESIDUES 77-162)	Mutation：H142F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；293 K；0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.29 Å R-free 0.273
4HOP Crystal structure of the computationally designed NNOS-Syntrophin complex Deposited 2012-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 77–162（86 aa） Fragment：PDZ DOMAIN (RESIDUES 77-162)	Mutation：H142F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；293 K；0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.29 Å R-free 0.273

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

View Construct and Data Evidence

UniProt name	SNA1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 2–264

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	1z87
Deposition date deposition_date	2005-03-30
Structure title title	solution structure of the split PH-PDZ Supramodule of alpha-Syntrophin
Keywords keywords	Alpha-1-syntrophin, PROTEIN BINDING; PROTEIN BINDING
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	27.63 Å
Radius of gyration Rg (electron density) rg_electron	27.21 Å
Forward intensity I(0) i0	2580520000.00
Molecular weight molecular_weight	415250.0 kDa
Excluded volume excluded_volume	515890 Å³
Envelope volume envelope_volume	183050 Å³
Hydration-shell volume shell_volume	47972 Å³
Envelope diameter envelope_diameter	105.4 Å
Shell Rg shell_rg	39.24 Å
Envelope Rg envelope_rg	30.69 Å
Shape Rg shape_rg	27.19 Å
Total Rg total_rg	27.58 Å
Total atoms total_atoms	58590
Residues n_residues	3945
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	91.3 Å
Rg (real space) rg_real	27.70 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	2.5810e+09
I(0) uncertainty (real space) i0_real_error	3.5980e+07
Rg (reciprocal space) rg_reciprocal	27.68 Å
I(0) (reciprocal space) i0_reciprocal	2580000000.0000
Solution quality estimate total_estimate	0.7975
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.622
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	180300000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1z87A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	1z87A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Description description	Alpha-1-syntrophin
Molecular weight formula_weight	27716.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	58590

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

fit	/app/data/saxs_computation/z8/1z87/1z87.fit
pddf	/app/data/pr_computation/z8/1z87/1z87.pr.out
profile	/app/data/saxs_computation/z8/1z87/1z87.dat

solution structure of the split PH-PDZ Supramodule of alpha-Syntrophin

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

Alpha-1-syntrophin

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)