SAXSdb — 7jvx

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

Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN

Homo sapiens

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 1–403	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；300 mM citrate	Resolution 3.20 Å R-free 0.296

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 7JVX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5R Crystal Structure of the PTEN Tumor Suppressor Deposited 1999-10-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–285（279 aa） Fragment：RESIDUES 7-353 Chain A 310–353（44 aa） Fragment：RESIDUES 7-353	Mutation：RESIDUES 286-309 ARE REPLACED BY VAL Mutation：RESIDUES 286-309 ARE REPLACED BY VAL	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；NA/K TARTRATE, 5% GLYCEROL, 100MM TRIS-CL, 10MM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.276
2KYL Solution structure of MAST2-PDZ complexed with the C-terminus of PTEN Deposited 2010-06-01	Different construct Different oligomeric state 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 391–403（13 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.6mM [U-100% 13C; U-100% 15N] PDZ-domain-1, 1.2mM PTEN-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4O1V SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer Deposited 2013-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 354–368（15 aa） Fragment：UNP residues 354-368	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris, 100 mM sodium malonate, 36% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.221
5BUG Crystal structure of human phosphatase PTEN oxidized by H2O2 Deposited 2015-06-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain A 14–351（338 aa） Fragment：PTEN wt 14-351 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.40 Å R-free 0.211
5BUG Crystal structure of human phosphatase PTEN oxidized by H2O2 Deposited 2015-06-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain B 14–351（338 aa） Fragment：PTEN wt 14-351 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.40 Å R-free 0.211
5BUG Crystal structure of human phosphatase PTEN oxidized by H2O2 Deposited 2015-06-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain C 14–351（338 aa） Fragment：PTEN wt 14-351 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.40 Å R-free 0.211
5BUG Crystal structure of human phosphatase PTEN oxidized by H2O2 Deposited 2015-06-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain D 14–351（338 aa） Fragment：PTEN wt 14-351 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.40 Å R-free 0.211
5BZX Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	VO4 VANADATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.50 Å R-free 0.204
5BZX Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.50 Å R-free 0.204
5BZX Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	VO4 VANADATE ION × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.50 Å R-free 0.204
5BZX Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol	Resolution 2.50 Å R-free 0.204
5BZZ Crystal structure of human phosphatase PTEN in its reduced state Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol	Resolution 2.20 Å R-free 0.221
5BZZ Crystal structure of human phosphatase PTEN in its reduced state Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol	Resolution 2.20 Å R-free 0.221
5BZZ Crystal structure of human phosphatase PTEN in its reduced state Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol	Resolution 2.20 Å R-free 0.221
5BZZ Crystal structure of human phosphatase PTEN in its reduced state Deposited 2015-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 14–351（338 aa） Fragment：PTEN wt 7-353 delta 286-309	Mutation：Deletion 286-309	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol	Resolution 2.20 Å R-free 0.221
7JUK Crystal structure of PTEN with a tetra-phosphorylated tail (4p-crPTEN-13sp-T2, SDTTDSDPENEG) Deposited 2020-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–285（279 aa） Chain A 310–353（44 aa） Chain A 378–390（13 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.2 M DL-malic acid	Resolution 3.15 Å R-free 0.289
7JUL Crystal structure of non phosphorylated PTEN (n-crPTEN-13sp-T1, SDTTDSDPENEG) Deposited 2020-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–285（279 aa） Chain A 310–353（44 aa） Chain A 378–390（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；1:1 volume of well solution: 100 mM Bis-Tris propane pH 7.0, 1.2 M DL-malic acid	Resolution 2.53 Å R-free 0.234
7PC7 The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN Deposited 2021-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 394–403（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris 8.5, 22 % v/v PEG Smear Broad	Resolution 2.10 Å R-free 0.218
7PC7 The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN Deposited 2021-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 394–403（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris 8.5, 22 % v/v PEG Smear Broad	Resolution 2.10 Å R-free 0.218
8X3S Crystal structure of human WDR5 in complex with PTEN Deposited 2023-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 115–148（34 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 lithium sulfate monohydrate, 0.1 M HEPES at pH 7.5, 25% w/v polyethylene glycol 3350	Resolution 1.87 Å R-free 0.259

10 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTEN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–422； UniProt 1–403

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	7jvx
Deposition date deposition_date	2020-08-24
Structure title title	Crystal structure of PTEN (aa 7-353 followed by spacer TGGGSGGTGGGSGGTGGGCY ligated to peptide pSDpTpTDpSDPENEPFDED)
Keywords keywords	;phosphatase, Phosphatidylinositol 3, 4, 5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN, SIGNALING PROTEIN ;; SIGNALING 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	22.71 Å
Radius of gyration Rg (electron density) rg_electron	21.64 Å
Forward intensity I(0) i0	23214900.00
Molecular weight molecular_weight	37433.0 kDa
Excluded volume excluded_volume	47095 Å³
Envelope volume envelope_volume	56497 Å³
Hydration-shell volume shell_volume	22043 Å³
Envelope diameter envelope_diameter	75.0 Å
Shell Rg shell_rg	27.87 Å
Envelope Rg envelope_rg	21.78 Å
Shape Rg shape_rg	21.62 Å
Total Rg total_rg	22.49 Å
Total atoms total_atoms	2639
Residues n_residues	314
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	72.2 Å
Rg (real space) rg_real	22.69 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.3210e+07
I(0) uncertainty (real space) i0_real_error	2.8560e+05
Rg (reciprocal space) rg_reciprocal	22.70 Å
I(0) (reciprocal space) i0_reciprocal	23210000.0000
Solution quality estimate total_estimate	0.9031
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.323
Kurtosis Kurtosis kurtosis	-0.426
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4862000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.979

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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	Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Molecular weight formula_weight	48555.5 kDa
EC 编号 ec_number	3.1.3.16,3.1.3.48,3.1.3.67
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	2639

MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSTGGGSGGTGGGSGGTGGGCDTTDSDPENEPFDEDQHTQITKV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	113.390 Å
Unit-cell length b length_b	113.390 Å
Unit-cell length c length_c	57.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.2472
R_work r_work	0.2444
R_free r_free	0.2965

fit	/app/data/saxs_computation/jv/7jvx/7jvx.fit
pddf	/app/data/pr_computation/jv/7jvx/7jvx.pr.out
profile	/app/data/saxs_computation/jv/7jvx/7jvx.dat

Crystal structure of PTEN (aa 7-353 followed by spacer TGGGSGGTGGGSGGTGGGCY ligated to peptide pSDpTpTDpSDPENEPFDED)

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

Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)