SAXSdb — 3o5n

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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 H； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 637–744	Fragment：PDZ domain, residues 637-744	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
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 637–744	Fragment：PDZ domain, residues 637-744	No other associated polymer	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
9	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 637–744 Chain H； UniProt 637–744	Fragment：PDZ domain, residues 637-744	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

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 3O5N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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
9KSQ Crystal Structure of the mouse Shank3 SAM domain Deposited 2024-11-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1654–1730（77 aa）	Not recorded	No recorded non-water small molecule	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

4 other PDB entries and 8 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 5–112； UniProt 637–744 Author chain B； PDBConstruct 5–112； UniProt 637–744 Author chain C； PDBConstruct 5–112； UniProt 637–744 Author chain D； PDBConstruct 5–112； UniProt 637–744 Author chain E； PDBConstruct 5–112； UniProt 637–744 Author chain F； PDBConstruct 5–112； UniProt 637–744 Author chain G； PDBConstruct 5–112； UniProt 637–744 Author chain H； PDBConstruct 5–112； UniProt 637–744

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	3o5n
Deposition date deposition_date	2010-07-28
Structure title title	Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders
Keywords keywords	PDZ domain, Protein-protein interaction, GKAP, postsynaptic density, PROTEIN BINDING; PROTEIN BINDING
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	33.57 Å
Radius of gyration Rg (electron density) rg_electron	32.90 Å
Forward intensity I(0) i0	108446000.00
Molecular weight molecular_weight	85166.0 kDa
Excluded volume excluded_volume	108020 Å³
Envelope volume envelope_volume	148190 Å³
Hydration-shell volume shell_volume	38868 Å³
Envelope diameter envelope_diameter	121.5 Å
Shell Rg shell_rg	38.10 Å
Envelope Rg envelope_rg	32.76 Å
Shape Rg shape_rg	32.88 Å
Total Rg total_rg	33.43 Å
Total atoms total_atoms	6023
Residues n_residues	772
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	113.8 Å
Rg (real space) rg_real	33.53 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.0840e+08
I(0) uncertainty (real space) i0_real_error	1.6530e+06
Rg (reciprocal space) rg_reciprocal	33.56 Å
I(0) (reciprocal space) i0_reciprocal	108400000.0000
Solution quality estimate total_estimate	0.8880
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.2 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16510000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SH3 and multiple ankyrin repeat domains protein 3
Molecular weight formula_weight	12205.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	6346

GAASSDYVIDDKVAILQKRDHEGFGFVLRGAKAETPIEEFTPTPAFPALQYLESVDVEGVAWRAGLRTGDFLIEVNGVNVVKVGHKQVVGLIRQGGNRLVMKVVSVTRKPEE

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	(3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid
Molecular weight formula_weight	304.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	290

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3o5na_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5nb_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5nc_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5nd_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5ne_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5nf_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5ng_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3o5nh_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

CATH v4.4 (8 domains)

Domain ID domain_id	3o5nA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3o5nH00
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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Unit-cell length a length_a	55.954 Å
Unit-cell length b length_b	64.063 Å
Unit-cell length c length_c	101.924 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	33.970 Å
R factor r_factor	0.2356
R_work r_work	0.2330
R_free r_free	0.2830

fit	/app/data/saxs_computation/o5/3o5n/3o5n.fit
pddf	/app/data/pr_computation/o5/3o5n/3o5n.pr.out
profile	/app/data/saxs_computation/o5/3o5n/3o5n.dat

Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders

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