SAXSdb — 5izu

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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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 533–665 Chain C； UniProt 533–665	Fragment：UNP residues 533-665	peptide from Disks large-associated protein 3 × 2 （Q6PFD5）	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

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 5IZU	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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
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 mutation/modification Different oligomeric state 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 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 7–139； UniProt 533–665 Author chain C； PDBConstruct 7–139； UniProt 533–665

peptide from Disks large-associated protein 3

OrganismNot specified

UniProt Q6PFD5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 963–977 Chain D； UniProt 963–977	Fragment：UNP residues 963-977	SH3 and multiple ankyrin repeat domains protein 3 × 2 （Q4ACU6）	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

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	DLGP3_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–15； UniProt 963–977 Author chain D； PDBConstruct 1–15； UniProt 963–977

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	5izu
Deposition date deposition_date	2016-03-26
Structure title title	A new binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function
Keywords keywords	Shank, SAPAP, PDZ, extension, synapse, specific interaction, 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	22.38 Å
Radius of gyration Rg (electron density) rg_electron	21.36 Å
Forward intensity I(0) i0	15290200.00
Molecular weight molecular_weight	30210.0 kDa
Excluded volume excluded_volume	38197 Å³
Envelope volume envelope_volume	46918 Å³
Hydration-shell volume shell_volume	18984 Å³
Envelope diameter envelope_diameter	73.4 Å
Shell Rg shell_rg	27.27 Å
Envelope Rg envelope_rg	21.32 Å
Shape Rg shape_rg	21.35 Å
Total Rg total_rg	22.26 Å
Total atoms total_atoms	2137
Residues n_residues	278
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	73.4 Å
Rg (real space) rg_real	22.34 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.5290e+07
I(0) uncertainty (real space) i0_real_error	2.2160e+05
Rg (reciprocal space) rg_reciprocal	22.35 Å
I(0) (reciprocal space) i0_reciprocal	15290000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.526
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3335000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.999

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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	15565.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2232

GPGSEFDTRHETREDRTKRLFRHYTVGSYDSLTSHSDYVIDDKVAILQKRDHEGFGFVLRGAKAETPIEEFTPTPAFPALQYLESVDVEGVAWRAGLRTGDFLIEVNGVNVVKVGHKQVVGLIRQGGNRLVMKVVSVTR

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	peptide from Disks large-associated protein 3
Molecular weight formula_weight	1719.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

ADSIEIYIPEAQTRL

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5izuC01
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	72.824 Å
Unit-cell length b length_b	72.824 Å
Unit-cell length c length_c	116.360 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	12

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	2.494 Å
Low-resolution limit resolution_low	42.763 Å
R factor r_factor	0.1863
R_work r_work	0.1831
R_free r_free	0.2506

fit	/app/data/saxs_computation/iz/5izu/5izu.fit
pddf	/app/data/pr_computation/iz/5izu/5izu.pr.out
profile	/app/data/saxs_computation/iz/5izu/5izu.dat

A new binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function

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

peptide from Disks large-associated 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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)