SAXSdb — 1vj6

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

protein-tyrosine-phosphatase (nonreceptor type 13)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1350–1443	Fragment：PDZ2 domain	Adenomatous polyposis coli protein × 1 （Q61315）	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：1mM PDZ2 protein, U-15N,13C; 3mM APC peptide, unlabelled \| 50 mM KH2PO4/K2HPO4 50 mM KCl, pH 6.8, H2O/D2O (95%/5%)	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 1VJ6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GM1 Second PDZ Domain (PDZ2) of PTP-BL Deposited 2001-09-06	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1351–1444（94 aa） Fragment：PDZ2	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1	Resolution not provided
1OZI The alternatively spliced PDZ2 domain of PTP-BL Deposited 2003-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1351–1444（94 aa） Fragment：PDZ2 of PTP-BL	Mutation：INS (VLFDK-G36)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 1.4mM PDZ2_AS, 13C/15N labelled, 50mM potassium phosphate buffer, 50mM KCl \| 95% H20, 5% D20	Resolution not provided
6GBD Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain Deposited 2018-04-13	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1475–1588（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) PBS；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] PDZ3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-99% 15N] PDZ3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6GBE Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex Deposited 2018-04-13	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1475–1588（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) PBS；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	PTN13_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–102； UniProt 1350–1443

Adenomatous polyposis coli protein

OrganismNot specified

UniProt Q61315

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 2834–2845	Fragment：C-terminus of APC	protein-tyrosine-phosphatase (nonreceptor type 13) × 1 （Q64512）	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：1mM PDZ2 protein, U-15N,13C; 3mM APC peptide, unlabelled \| 50 mM KH2PO4/K2HPO4 50 mM KCl, pH 6.8, H2O/D2O (95%/5%)	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 1VJ6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9W9I Cryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC Deposited 2025-08-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 338–1010（673 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APC_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 2834–2845

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	1vj6
Deposition date deposition_date	2004-02-03
Structure title title	PDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein
Keywords keywords	PDZ, complex, APC, protein-protein interaction, PTP-BL, C-terminus, Hydrolase-Signaling Protein COMPLEX; Hydrolase/Signaling Protein
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	12.87 Å
Radius of gyration Rg (electron density) rg_electron	12.58 Å
Forward intensity I(0) i0	1888620000.00
Molecular weight molecular_weight	369780.0 kDa
Excluded volume excluded_volume	464110 Å³
Envelope volume envelope_volume	25133 Å³
Hydration-shell volume shell_volume	14153 Å³
Envelope diameter envelope_diameter	47.6 Å
Shell Rg shell_rg	20.92 Å
Envelope Rg envelope_rg	15.18 Å
Shape Rg shape_rg	12.56 Å
Total Rg total_rg	12.77 Å
Total atoms total_atoms	52815
Residues n_residues	3535
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	39.5 Å
Rg (real space) rg_real	12.77 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	1.8890e+09
I(0) uncertainty (real space) i0_real_error	1.9650e+07
Rg (reciprocal space) rg_reciprocal	12.77 Å
I(0) (reciprocal space) i0_reciprocal	1889000000.0000
Solution quality estimate total_estimate	0.8121
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.013
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	202400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; 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)

Entity 1 Entity 1 polymer

Description description	protein-tyrosine-phosphatase (nonreceptor type 13)
Molecular weight formula_weight	10858.3 kDa
EC 编号 ec_number	3.1.3.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	52815

MHHHHHHMKPGDTFEVELAKTDGSLGISVTGGVNTSVRHGGIYVKAIIPKGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQVP

来源 Source

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)

Entity 2 Entity 2 polymer

Description description	Adenomatous polyposis coli protein
Molecular weight formula_weight	1336.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KRHSGSYLVTSV

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vj6a1
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	d1vj6a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1vj6A00
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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fit	/app/data/saxs_computation/vj/1vj6/1vj6.fit
pddf	/app/data/pr_computation/vj/1vj6/1vj6.pr.out
profile	/app/data/saxs_computation/vj/1vj6/1vj6.dat

PDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein

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

protein-tyrosine-phosphatase (nonreceptor type 13)

State in the Current Structure

Other States of the Same Protein in the Database

Adenomatous polyposis coli 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

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)