SAXSdb — 9ksq

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

SH3 and multiple ankyrin repeat domains protein 3

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 1654–1730	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20% v/v 2-Propanol	Resolution 2.79 Å R-free 0.255

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 9KSQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	BR0 (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
3O5N Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders Deposited 2010-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 637–744（108 aa） Fragment：PDZ domain, residues 637-744 Chain H 637–744（108 aa） Fragment：PDZ domain, residues 637-744	Not recorded	BR0 (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.83 Å R-free 0.283
5IZU A new binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function Deposited 2016-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 533–665（133 aa） Fragment：UNP residues 533-665 Chain C 533–665（133 aa） Fragment：UNP residues 533-665	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；289 K；0.1 M Bis-Tris, 3.0 M NaCl	Resolution 2.49 Å R-free 0.251
6KYH Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas Deposited 2019-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 8–362（355 aa） Fragment：NTD-ANK tandem	Mutation：A42K,L231R,F304Y	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000	Resolution 3.30 Å R-free 0.257
6KYH Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas Deposited 2019-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 8–362（355 aa） Fragment：NTD-ANK tandem	Mutation：A42K,L231R,F304Y	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000	Resolution 3.30 Å R-free 0.257
6KYH Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas Deposited 2019-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 8–362（355 aa） Fragment：NTD-ANK tandem	Mutation：A42K,L231R,F304Y	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000	Resolution 3.30 Å R-free 0.257
6KYH Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas Deposited 2019-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 8–362（355 aa） Fragment：NTD-ANK tandem	Mutation：A42K,L231R,F304Y	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000	Resolution 3.30 Å R-free 0.257
6KYK Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 Deposited 2019-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–368（368 aa） Fragment：NTD-ANK tandem	Mutation：L231R,F304Y	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500	Resolution 2.82 Å R-free 0.300
6KYK Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 Deposited 2019-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–368（368 aa） Fragment：NTD-ANK tandem	Mutation：L231R,F304Y	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500	Resolution 2.82 Å R-free 0.300

4 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SHAN3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–83； UniProt 1654–1730

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	9ksq
Deposition date deposition_date	2024-11-30
最后修订 last_revision	2025-12-03
Structure title title	Crystal Structure of the mouse Shank3 SAM domain
Keywords keywords	Self oligomerized domain, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	12.93 Å
Radius of gyration Rg (electron density) rg_electron	11.42 Å
Forward intensity I(0) i0	1641810.00
Molecular weight molecular_weight	8480.0 kDa
Excluded volume excluded_volume	10540 Å³
Envelope volume envelope_volume	11770 Å³
Hydration-shell volume shell_volume	8949 Å³
Envelope diameter envelope_diameter	38.3 Å
Shell Rg shell_rg	16.85 Å
Envelope Rg envelope_rg	11.69 Å
Shape Rg shape_rg	11.36 Å
Total Rg total_rg	12.91 Å
Total atoms total_atoms	601
Residues n_residues	72
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	40.0 Å
Rg (real space) rg_real	12.82 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.6420e+06
I(0) uncertainty (real space) i0_real_error	1.7480e+04
Rg (reciprocal space) rg_reciprocal	12.83 Å
I(0) (reciprocal space) i0_reciprocal	1642000.0000
Solution quality estimate total_estimate	0.8023
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.033
Kurtosis Kurtosis kurtosis	-0.292
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	290600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; 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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8. Citations (1)

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Unit-cell length a length_a	63.464 Å
Unit-cell length b length_b	63.464 Å
Unit-cell length c length_c	49.083 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	31.730 Å
R factor r_factor	0.2039
R_work r_work	0.2010
R_free r_free	0.2546

Description description	SH3 and multiple ankyrin repeat domains protein 3
Molecular weight formula_weight	9589.7 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	609

Crystal Structure of the mouse Shank3 SAM domain

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

SH3 and multiple ankyrin repeat domains protein 3

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/ks/9ksq/9ksq.fit
pddf	/app/data/pr_computation/ks/9ksq/9ksq.pr.out
profile	/app/data/saxs_computation/ks/9ksq/9ksq.dat