SAXSdb — 5jnw

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

Low molecular weight phosphotyrosine protein phosphatase

Bos taurus

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 2–158	Mutation：W49Y N50E	VO4 VANADATE ION × 1 6LJ 2-(4-{[3-(piperidin-1-yl)propyl]amino}quinolin-2-yl)benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 6.5；293 K；20% PEG 3350, 0.2 M NaCl, Bis Tris	Resolution 1.86 Å R-free 0.209

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 5JNW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BVH SOLUTION STRUCTURE OF A LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE Deposited 1994-05-03	Different construct Different mutation/modification 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 1–157（157 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1C0E Active Site S19A Mutant of Bovine Heart Phosphotyrosyl Phosphatase Deposited 1999-07-15	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 1–157（157 aa）	Mutation：S19A	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 4000, TRIS BUFFER, pH 7.00	Resolution 2.20 Å R-free 0.244
1C0E Active Site S19A Mutant of Bovine Heart Phosphotyrosyl Phosphatase Deposited 1999-07-15	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 1–157（157 aa）	Mutation：S19A	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 4000, TRIS BUFFER, pH 7.00	Resolution 2.20 Å R-free 0.244
1DG9 CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT PTPASE COMPLEXED WITH HEPES Deposited 1999-11-23	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 1–157（157 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；20% PEG4k, 10% 2-propanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION	Resolution 1.90 Å
1PHR THE CRYSTAL STRUCTURE OF A LOW MOLECULAR PHOSPHOTYROSINE PROTEIN PHOSPHATASE Deposited 1994-07-05	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 1–157（157 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.232
1PNT CRYSTAL STRUCTURE OF BOVINE HEART PHOSPHOTYROSYL PHOSPHATASE AT 2.2 ANGSTROMS RESOLUTION Deposited 1994-08-05	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 1–157（157 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1Z12 Crystal Structure of Bovine Low Molecular Weight PTPase Complexed with Vanadate Deposited 2005-03-03	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 1–157（157 aa）	Not recorded	VO4 VANADATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG 4000, HEPES, Isopropanol, Na2VO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.20 Å
1Z13 Crystal Structure of Bovine Low Molecular Weight PTPase Complexed with Molybdate Deposited 2005-03-03	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 1–157（157 aa）	Not recorded	MOO MOLYBDATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG 4000, HEPES, Isopropanol, Na2MoO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.20 Å
5JNV Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with HEPES Deposited 2016-04-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：W49Y N50E	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 DMS DIMETHYL SULFOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；20% PEG 3350, 0.2 M NaCl, Bis Tris, HEPES	Resolution 1.60 Å R-free 0.200

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPAC_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–159； UniProt 2–158

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	5jnw
Deposition date deposition_date	2016-04-30
Structure title title	Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with vanadate and uncompetitive inhibitor
Keywords keywords	protein tyrosine phosphatase, hydrolase, LMW-PTP, LMPTP, hydrolase-hydrolase INHIBITOR complex; hydrolase/hydrolase INHIBITOR
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	16.03 Å
Radius of gyration Rg (electron density) rg_electron	14.82 Å
Forward intensity I(0) i0	6600280.00
Molecular weight molecular_weight	18056.0 kDa
Excluded volume excluded_volume	22362 Å³
Envelope volume envelope_volume	25306 Å³
Hydration-shell volume shell_volume	14208 Å³
Envelope diameter envelope_diameter	52.0 Å
Shell Rg shell_rg	20.94 Å
Envelope Rg envelope_rg	15.21 Å
Shape Rg shape_rg	14.83 Å
Total Rg total_rg	15.92 Å
Total atoms total_atoms	1264
Residues n_residues	154
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	53.2 Å
Rg (real space) rg_real	15.91 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	6.6000e+06
I(0) uncertainty (real space) i0_real_error	7.5680e+04
Rg (reciprocal space) rg_reciprocal	15.93 Å
I(0) (reciprocal space) i0_reciprocal	6600000.0000
Solution quality estimate total_estimate	0.8760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.124
Kurtosis Kurtosis kurtosis	-0.403
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1513000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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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	Low molecular weight phosphotyrosine protein phosphatase
Molecular weight formula_weight	18082.4 kDa
EC 编号 ec_number	3.1.3.48
Mutation mutation	W49Y N50E
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	1501

GSAEQVTKSVLFVCLGNICRSPIAEAVFRKLVTDQNISDNWVIDSGAVSDYEVGRSPDPRAVSCLRNHGINTAHKARQVTKEDFVTFDYILCMDESNLRDLNRKSNQVKNCRAKIELLGSYDPQKQLIIEDPYYGNDADFETVYQQCVRCCRAFLEKVR

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	VANADATE ION
Molecular weight formula_weight	114.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-(4-{[3-(piperidin-1-yl)propyl]amino}quinolin-2-yl)benzonitrile
Molecular weight formula_weight	370.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5jnwa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamily	c.44.1 — Phosphotyrosine protein phosphatases I
Family Family family	c.44.1.1 — Low-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (1 domains)

Domain ID domain_id	5jnwA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (1)

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Unit-cell length a length_a	60.347 Å
Unit-cell length b length_b	125.493 Å
Unit-cell length c length_c	45.251 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	36.700 Å
R factor r_factor	0.1683
R_work r_work	0.1663
R_free r_free	0.2095

fit	/app/data/saxs_computation/jn/5jnw/5jnw.fit
pddf	/app/data/pr_computation/jn/5jnw/5jnw.pr.out
profile	/app/data/saxs_computation/jn/5jnw/5jnw.dat

Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with vanadate and uncompetitive inhibitor

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

Low molecular weight phosphotyrosine protein phosphatase

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