SAXSdb — 6gbe

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

Tyrosine-protein phosphatase non-receptor 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 1475–1588	Not recorded	Serine/threonine-protein kinase N2 × 1 （Q16513）	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

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 6GBE	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
1VJ6 PDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein Deposited 2004-02-03	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1350–1443（94 aa） Fragment：PDZ2 domain	Not recorded	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 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
6GBD Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain Deposited 2018-04-13	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

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 1–114； UniProt 1475–1588

Serine/threonine-protein kinase N2

OrganismNot specified

UniProt Q16513

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 973–984	Not recorded	Tyrosine-protein phosphatase non-receptor type 13 × 1 （Q64512）	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

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 6GBE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4CRS Human Protein Kinase N2 (PKN2, PRKCL2) in complex with ATPgammaS Deposited 2014-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 646–984（339 aa） Fragment：KINASE DOMAIN, RESIDUES 646-984	Non-standard monomer：Yes (specific site not provided by mmCIF)	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；2.3M AMMONIUM SULPHATE, 0.1M CITRATE PH 5.8, 0.2M SODIUM/POTASSIUM TARTRATE	Resolution 2.75 Å R-free 0.262
4RRV Crystal structure of PDK1 in complex with ATP and PIFtide Deposited 2014-11-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 969–983（15 aa） Fragment：PIFtide (PRK2 hydrophobic motif, UNP residues 969-983)	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21 mg/mL protein in 25 mM Tris, pH 7.5, 0.5 M sodium chloride, 1 mM DTT, 15 mM EDTA, 15 mM ATP, precipitant: 0.1 M HEPES, pH 7.5, 1.2 M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 1.41 Å R-free 0.163
6CCY Crystal structure of Akt1 in complex with a selective inhibitor Deposited 2018-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 969–983（15 aa）	Mutation：N199S, S396P, E397S, T433V Non-standard monomer：Yes (specific site not provided by mmCIF)	EX4 (5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；16% PEG 3350 and 200mM Ammonium Formate	Resolution 2.18 Å R-free 0.276

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKN2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 973–984

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	6gbe
Deposition date deposition_date	2018-04-13
Structure title title	Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex
Keywords keywords	PTPN13, PDZ3, 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	16.25 Å
Radius of gyration Rg (electron density) rg_electron	15.89 Å
Forward intensity I(0) i0	1089640000.00
Molecular weight molecular_weight	284760.0 kDa
Excluded volume excluded_volume	358440 Å³
Envelope volume envelope_volume	52718 Å³
Hydration-shell volume shell_volume	21825 Å³
Envelope diameter envelope_diameter	69.2 Å
Shell Rg shell_rg	27.05 Å
Envelope Rg envelope_rg	20.63 Å
Shape Rg shape_rg	15.89 Å
Total Rg total_rg	16.13 Å
Total atoms total_atoms	40060
Residues n_residues	2620
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	59.0 Å
Rg (real space) rg_real	16.19 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.0900e+09
I(0) uncertainty (real space) i0_real_error	1.2520e+07
Rg (reciprocal space) rg_reciprocal	16.20 Å
I(0) (reciprocal space) i0_reciprocal	1090000000.0000
Solution quality estimate total_estimate	0.7469
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.116
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	569600.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; 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	Tyrosine-protein phosphatase non-receptor type 13
Molecular weight formula_weight	12690.3 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	40060

TPHVKDYSFVTEDNTFEVKLFKNSSGLGFSFSREDNLIPEQINGSIVRVKKLFPGQPAAESGKIDVGDVILKVNGAPLKGLSQQDVISALRGTAPEVSLLLCRPAPGVLPEIDTPGNSS

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 polymer

Description description	Serine/threonine-protein kinase N2
Molecular weight formula_weight	1582.8 kDa
EC 编号 ec_number	2.7.11.13
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MFRDFDYIADWC

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8. Citations (1)

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fit	/app/data/saxs_computation/gb/6gbe/6gbe.fit
pddf	/app/data/pr_computation/gb/6gbe/6gbe.pr.out
profile	/app/data/saxs_computation/gb/6gbe/6gbe.dat

Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex

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

Tyrosine-protein phosphatase non-receptor type 13

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase N2

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)