SAXSdb — 3o4s

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

Tyrosine-protein phosphatase non-receptor type 7

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 65–360	Fragment：UNP RESIDUES 65-360 Mutation：S72D	SO4 SULFATE ION × 6 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.7-1.9M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.212

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 3O4S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZC0 Crystal structure of human hematopoietic tyrosine phosphatase (HePTP) catalytic domain Deposited 2005-04-09	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 65–360（296 aa） Fragment：Catalytic Phosphatase Domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；Sodium/potassium phosphate, acetate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.85 Å R-free 0.186
2GP0 HePTP Catalytic Domain (residues 44-339), S225D mutant Deposited 2006-04-15	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 65–360（296 aa） Fragment：Catalytic Domain (residues 65-360)	Mutation：S225D	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；277 K；K/Na Phosphate, Ammonium Acetate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.206
2GPH Docking motif interactions in the MAP kinase ERK2 Deposited 2006-04-17	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 B 37–52（16 aa）	Mutation：C52V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 4000, 10% isopropanol, 0.1M sodium HEPES, pH 7.5, temperature 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.90 Å R-free 0.263
2HVL Crystal structure of the HePTP catalytic domain C270S mutant Deposited 2006-07-29	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 65–360（296 aa）	Mutation：C270S	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；277 K；Sodium/Potassium phosphate, acetate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.228
2QDC Crystal structure of the HePTP catalytic domain D236A mutant Deposited 2007-06-20	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 65–360（296 aa） Fragment：Catalytic domain (residues 65-360)	Mutation：D236A	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1 M ACETIC ACID, 2.0 M SODIUM/POTASSIUM PHOSPHATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.190
2QDM Crystal structure of the HePTP catalytic domain C270S/D236A/Q314A mutant Deposited 2007-06-21	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 65–360（296 aa） Fragment：Catalytic domain (residues 65-360)	Mutation：C270S, D236A, Q314A	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；1.5 M AMMONIUM CHLORIDE, 0.1 M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.05 Å R-free 0.208
2QDP Crystal structure of the HePTP catalytic domain C270S mutant crystallized in ammonium acetate Deposited 2007-06-21	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 65–360（296 aa） Fragment：Catalytic domain (residues 65-360)	Mutation：C270S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.07 M AMMONIUM ACETATE, 0.07 M BIS-TRIS, 12% POLYETHYLENE GLYCOL 10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.72 Å R-free 0.227
3D42 Crystal structure of HePTP in complex with a monophosphorylated Erk2 peptide Deposited 2008-05-13	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 65–360（296 aa） Fragment：Catalytic domain (UNP residues 65-360)	Mutation：T106D, C270S	TAR D(-)-TARTARIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；277 K；0.2 M AMMONIUM TARTRATE DIBASIC, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.46 Å R-free 0.241
3D44 Crystal structure of HePTP in complex with a dually phosphorylated Erk2 peptide mimetic Deposited 2008-05-13	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 65–360（296 aa） Fragment：Catalytic domain (UNP residues 65-360)	Mutation：T106D, C270S	CL CHLORIDE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.0 M LITHIUM CHLORIDE, 0.1 M CITRATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.204
3O4T Crystal Structure of HePTP with an Open WPD Loop and Partially Depleted Active Site Deposited 2010-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–360（296 aa） Fragment：UNP RESIDUES 65-360	Mutation：S72D	SO4 SULFATE ION × 1 TAR D(-)-TARTARIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.7-1.9M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.253
3O4U Crystal Structure of HePTP with an Atypically Open WPD Loop Deposited 2010-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–360（296 aa） Fragment：UNP RESIDUES 65-360	Mutation：S72D	TLA L(+)-TARTARIC ACID × 1 SRT S,R MESO-TARTARIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；1.7-1.9M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.243
8YP8 Structure of the p38alpha-pepHePTPm(16-31)(V31C ) complex Deposited 2024-03-15	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 B 37–52（16 aa）	Mutation：V31C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；0.1 M HEPES pH 7.8 0.6-0.8 M Sodium Citrate	Resolution 2.14 Å R-free 0.216

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTN7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–308； UniProt 65–360

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	3o4s
Deposition date deposition_date	2010-07-27
Structure title title	Crystal Structure of HePTP with a Closed WPD Loop and an Ordered E-Loop
Keywords keywords	HEPTP, HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT, LC-PTP, PTPN7, HYDROLASE; HYDROLASE
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	20.29 Å
Radius of gyration Rg (electron density) rg_electron	19.13 Å
Forward intensity I(0) i0	21190300.00
Molecular weight molecular_weight	34015.0 kDa
Excluded volume excluded_volume	42140 Å³
Envelope volume envelope_volume	49330 Å³
Hydration-shell volume shell_volume	21189 Å³
Envelope diameter envelope_diameter	65.8 Å
Shell Rg shell_rg	25.89 Å
Envelope Rg envelope_rg	19.61 Å
Shape Rg shape_rg	19.14 Å
Total Rg total_rg	20.01 Å
Total atoms total_atoms	2384
Residues n_residues	293
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	64.8 Å
Rg (real space) rg_real	20.21 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	2.1190e+07
I(0) uncertainty (real space) i0_real_error	2.7370e+05
Rg (reciprocal space) rg_reciprocal	20.23 Å
I(0) (reciprocal space) i0_reciprocal	21190000.0000
Solution quality estimate total_estimate	0.8926
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.266
Kurtosis Kurtosis kurtosis	-0.306
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5590000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase non-receptor type 7
Molecular weight formula_weight	35232.8 kDa
EC 编号 ec_number	3.1.3.48
Mutation mutation	S72D
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	2677

MGSDKIHHHHHHNTPREVTLHFLRTAGHPLTRWALQRQPPDPKQLEEEFLKIPSNFVSPEDLDIPGHASKDRYKTILPNPQSRVCLGRAQSQEDGDYINANYIRGYDGKEKVYIATQGPMPNTVSDFWEMVWQEEVSLIVMLTQLREGKEKCVHYWPTEEETYGPFQIRIQDMKECPEYTVRQLTIQYQEERRSVKHILFSAWPDHQTPESAGPLLRLVAEVEESPETAAHPGPIVVHCSAGIGRTGCFIATRIGCQQLKARGEVDILGIVCQLRLDRGGMIQTAEQYQFLHHTLALYAGQLPEEPSP

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3o4sa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3o4sA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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8. Citations (1)

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Unit-cell length a length_a	117.795 Å
Unit-cell length b length_b	39.130 Å
Unit-cell length c length_c	83.441 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1643
R_work r_work	0.1617
R_free r_free	0.2121

fit	/app/data/saxs_computation/o4/3o4s/3o4s.fit
pddf	/app/data/pr_computation/o4/3o4s/3o4s.pr.out
profile	/app/data/saxs_computation/o4/3o4s/3o4s.dat

Crystal Structure of HePTP with a Closed WPD Loop and an Ordered E-Loop

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

Tyrosine-protein phosphatase non-receptor type 7

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