SAXSdb — 3lny

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

Tyrosine-protein 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 heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1361–1456	Fragment：PDZ2 domain	Rap guanine nucleotide exchange factor 6 × 6 （Q8TEU7） 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

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 3LNY	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 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 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
1WCH Crystal structure of PTPL1 human tyrosine phosphatase mutated in colorectal cancer - evidence for a second phosphotyrosine substrate recognition pocket Deposited 2004-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2163–2477（315 aa） Fragment：RESIDUES 2163-2477	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION	Resolution 1.85 Å R-free 0.204
2M0Z cis form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative Deposited 2012-11-09	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 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 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 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
3PDZ SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP1E Deposited 1999-05-10	Different construct 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 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 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 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 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 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	PTN13_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–96； UniProt 1361–1456

Rap guanine nucleotide exchange factor 6

Homo sapiens

UniProt Q8TEU7

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain B； UniProt 1596–1601	Fragment：C-terminal residues 1596-1601	Tyrosine-protein phosphatase non-receptor type 13 × 6 （Q12923） 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

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 3LNY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2D93 Solution structure of the cNMP_binding domain of human Rap guanine nucleotide exchange factor 6 Deposited 2005-12-08	Different construct 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 265–385（121 aa） Fragment：cNMP_binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.06mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPGF6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–6； UniProt 1596–1601

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	3lny
Deposition date deposition_date	2010-02-03
Structure title title	Second PDZ domain from human PTP1E in complex with RA-GEF2 peptide
Keywords keywords	;PDZ2, Structural Genomics, Protein Structure Initiative, PSI-2, Center for Eukaryotic Structural Genomics, CESG, Cytoskeleton, Cell membrane, Guanine-nucleotide releasing factor, signaling protein-signaling protein complex ;; 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	14.02 Å
Radius of gyration Rg (electron density) rg_electron	12.42 Å
Forward intensity I(0) i0	2706560.00
Molecular weight molecular_weight	10656.0 kDa
Excluded volume excluded_volume	13098 Å³
Envelope volume envelope_volume	14850 Å³
Hydration-shell volume shell_volume	10312 Å³
Envelope diameter envelope_diameter	42.4 Å
Shell Rg shell_rg	17.99 Å
Envelope Rg envelope_rg	12.62 Å
Shape Rg shape_rg	12.40 Å
Total Rg total_rg	13.75 Å
Total atoms total_atoms	1487
Residues n_residues	100
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	43.8 Å
Rg (real space) rg_real	13.89 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	2.7070e+06
I(0) uncertainty (real space) i0_real_error	2.9710e+04
Rg (reciprocal space) rg_reciprocal	13.90 Å
I(0) (reciprocal space) i0_reciprocal	2707000.0000
Solution quality estimate total_estimate	0.8926
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.7 Å
Skewness Skewness skewness	0.035
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	398900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase non-receptor type 13
Molecular weight formula_weight	10020.3 kDa
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	1856

PKPGDIFEVELAKNDNSLGISVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQSPT

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 polymer

Description description	Rap guanine nucleotide exchange factor 6
Molecular weight formula_weight	631.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EQVSAV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 3 Entity 3 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3lnya_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

CATH v4.4 (1 domains)

Domain ID domain_id	3lnyA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	73.965 Å
Unit-cell length b length_b	73.965 Å
Unit-cell length c length_c	134.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	29.695 Å
R factor r_factor	0.1640
R_work r_work	0.1630
R_free r_free	0.1890

fit	/app/data/saxs_computation/ln/3lny/3lny.fit
pddf	/app/data/pr_computation/ln/3lny/3lny.pr.out
profile	/app/data/saxs_computation/ln/3lny/3lny.dat

Second PDZ domain from human PTP1E in complex with RA-GEF2 peptide

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

Rap guanine nucleotide exchange factor 6

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)