SAXSdb — 1wch

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

PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13

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 2163–2477	Fragment：RESIDUES 2163-2477	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION	Resolution 1.85 Å R-free 0.204

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 1WCH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5G SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP1E COMPLEXED WITH A PEPTIDE Deposited 1999-10-07	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 A 1361–1456（96 aa） Fragment：PDZ2 DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 0.15 M NACL；Pressure AMBIENT NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 0.15 M NACL；Pressure AMBIENT NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 0.15 M NACL；Pressure AMBIENT NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 0.15 M NACL；Pressure AMBIENT NMR sample composition 1.0-5.0 MM OF N15-LABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE NMR sample composition 1.0-5.0 MM OF UNLABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE NMR sample composition 1.0-5.0 MM OF UNLABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE NMR sample composition 1.0-5.0 MM OF DOUBLE-LABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE	Resolution not provided
1Q7X Solution structure of the alternatively spliced PDZ2 domain (PDZ2b) of PTP-Bas (hPTP1E) Deposited 2003-08-20	Different construct 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 1357–1464（108 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 150mM sodium chloride；Pressure ambient NMR sample composition 2mM PDZ2b U-15N, 13C; 50mM phosphate buffer with 150mM sodium chloride \| 92% H20, 8% D2O NMR sample composition 2mM PDZ2b U-15N; 50mM phosphate buffer with 150mM sodium chloride \| 92% H20, 8% D2O NMR sample composition 2mM PDZ2b unlabeled; 50mM phosphate buffer with 150mM sodium chloride \| 92% H20, 8% D2O	Resolution not provided
2M0Z cis form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative Deposited 2012-11-09	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 1361–1456（96 aa） Fragment：PDZ 2 domain residues 1361-1456	Mutation：S1381C, E1436C	33B 3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid} × 1	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.75 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 4.3 % C12E5, 1.8 % n-hexanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.75 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 8.5 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.75 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M10 trans form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative Deposited 2012-11-09	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 1361–1456（96 aa） Fragment：PDZ 2 domain residues 1361-1456	Mutation：S1381C, E1436C	33B 3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid} × 1	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.75 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 4.3 % C12E5, 1.8 % n-hexanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.75 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 8.5 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.75 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3LNX Second PDZ domain from human PTP1E Deposited 2010-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1361–1456（96 aa） Fragment：PDZ2 domain Chain B 1361–1456（96 aa） Fragment：PDZ2 domain Chain C 1361–1456（96 aa） Fragment：PDZ2 domain Chain D 1361–1456（96 aa） Fragment：PDZ2 domain Chain E 1361–1456（96 aa） Fragment：PDZ2 domain Chain F 1361–1456（96 aa） Fragment：PDZ2 domain	Not recorded	IOD IODIDE ION × 25 SCN THIOCYANATE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；28% PEG 3350, 0.2 M KI, 0.2 M NaSCN, 0.1 M NaAc, pH 4.5, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.64 Å R-free 0.237
3LNY Second PDZ domain from human PTP1E in complex with RA-GEF2 peptide Deposited 2010-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1361–1456（96 aa） Fragment：PDZ2 domain	Not recorded	SCN THIOCYANATE ION × 6 SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG 3350, 0.8 M (NH4)2SO4, 0.2 M NaSCN, 0.1 M Na citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.30 Å R-free 0.189
3PDZ SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP1E Deposited 1999-05-10	Different construct 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 1361–1456（96 aa） Fragment：PDZ2 DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Pressure 1 NMR sample composition 10% D2O/90% WATER	Resolution not provided
5GLJ Crystal Structure of PDZ1 Domain of Human Protein Tyrosine Phosphatase PTP-Bas Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1086–1178（93 aa） Fragment：PDZ1 Domain (UNP RESIDUES 1086-1178) Chain B 1086–1178（93 aa） Fragment：PDZ1 Domain (UNP RESIDUES 1086-1178) Chain C 1086–1178（93 aa） Fragment：PDZ1 Domain (UNP RESIDUES 1086-1178) Chain D 1086–1178（93 aa） Fragment：PDZ1 Domain (UNP RESIDUES 1086-1178)	Not recorded	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M Magnesium chloride hexahydrate , 0.1 M BIS-TRIS pH5.5, 25 % w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.206
7QCX Two-state liquid NMR Structure of a PDZ2 Domain from hPTP1E, apo form Deposited 2021-11-25	Different construct 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 1361–1456（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] PDZ2 domain from hPTP1E, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7QCY Two-state liquid NMR Structure of a PDZ2 Domain from hPTP1E, complexed with RA-GEF2 peptide Deposited 2021-11-25	Different construct 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 1361–1456（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 2 mM [U-100% 13C; U-100% 15N] PDZ2 domain, 2 mM RA-GEF2 peptide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7XTY Crystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide Deposited 2022-05-18	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 A 1362–1456（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；289 K；0.1M citric acid (pH 3.5), 3M NaCl	Resolution 2.10 Å R-free 0.240
7XTY Crystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide Deposited 2022-05-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1362–1456（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；289 K；0.1M citric acid (pH 3.5), 3M NaCl	Resolution 2.10 Å R-free 0.240

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

View Construct and Data Evidence

UniProt name	PTND_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–315； UniProt 2163–2477

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	1wch
Deposition date deposition_date	2004-11-16
Structure title title	Crystal structure of PTPL1 human tyrosine phosphatase mutated in colorectal cancer - evidence for a second phosphotyrosine substrate recognition pocket
Keywords keywords	;HYDROLASE, TYROSINE PHOSPHATASE, PHOSPHATE ION, COLORECTAL CANCER ALTERNATIVE SPLICING, COILED COIL, CYTOSKELETON, POLYMORPHISM, STRUCTURAL PROTEIN ;; 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	20.85 Å
Radius of gyration Rg (electron density) rg_electron	19.75 Å
Forward intensity I(0) i0	21879200.00
Molecular weight molecular_weight	35501.0 kDa
Excluded volume excluded_volume	44443 Å³
Envelope volume envelope_volume	51605 Å³
Hydration-shell volume shell_volume	21640 Å³
Envelope diameter envelope_diameter	71.2 Å
Shell Rg shell_rg	26.50 Å
Envelope Rg envelope_rg	20.22 Å
Shape Rg shape_rg	19.74 Å
Total Rg total_rg	20.65 Å
Total atoms total_atoms	2487
Residues n_residues	308
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	69.3 Å
Rg (real space) rg_real	20.80 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.1880e+07
I(0) uncertainty (real space) i0_real_error	2.5790e+05
Rg (reciprocal space) rg_reciprocal	20.81 Å
I(0) (reciprocal space) i0_reciprocal	21880000.0000
Solution quality estimate total_estimate	0.6880
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.319
Kurtosis Kurtosis kurtosis	-0.239
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5913000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.999; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13
Molecular weight formula_weight	36087.5 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	2801

HEDSDKDHSFLTNDELAVLPVVKVLPSGKYTGANLKSVIRVLRGLLDQGIPSKELENLQELKPLDQCLIGQTKENRRKNRYKNILPYDATRVPLGDEGGYINASFIKIPVGKEEFVYIACQGPLPTTVGDFWQMIWEQKSTVIAMMTQEVEGEKIKCQRYWPNILGKTTMVSNRLRLALVRMQQLKGFVVRAMTLEDIQTREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIHRSGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTRLQAEEEQ

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wcha_
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.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (1 domains)

Domain ID domain_id	1wchA00
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	99.707 Å
Unit-cell length b length_b	59.193 Å
Unit-cell length c length_c	66.075 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.05 °
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	1.850 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2040

fit	/app/data/saxs_computation/wc/1wch/1wch.fit
pddf	/app/data/pr_computation/wc/1wch/1wch.pr.out
profile	/app/data/saxs_computation/wc/1wch/1wch.dat

Crystal structure of PTPL1 human tyrosine phosphatase mutated in colorectal cancer - evidence for a second phosphotyrosine substrate recognition pocket

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

PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13

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