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6gbd

Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain

Method: SOLUTION NMR Dmax: 58.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PDZ3

Mus musculus

UniProt Q64512

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 1475–1588 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) PBS；Pressure 1 NMR sample composition：1.0 mM [U-99% 13C; U-99% 15N] PDZ3, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.5 mM [U-99% 15N] PDZ3, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 6GBD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GM1 Second PDZ Domain (PDZ2) of PTP-BL Deposited 2001-09-06 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1351–1444（94 aa） Fragment：PDZ2
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
Resolution not provided
1OZI The alternatively spliced PDZ2 domain of PTP-BL Deposited 2003-04-09 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1351–1444（94 aa） Fragment：PDZ2 of PTP-BL
Mutation：INS (VLFDK-G36) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1.4mM PDZ2_AS, 13C/15N labelled, 50mM potassium phosphate buffer, 50mM KCl | 95% H20, 5% D20
Resolution not provided
1VJ6 PDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein Deposited 2004-02-03 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1350–1443（94 aa） Fragment：PDZ2 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1mM PDZ2 protein, U-15N,13C; 3mM APC peptide, unlabelled | 50 mM KH2PO4/K2HPO4 50 mM KCl, pH 6.8, H2O/D2O (95%/5%)
Resolution not provided
6GBE Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex Deposited 2018-04-13 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1475–1588（114 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) PBS；Pressure 1
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN13_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–114； UniProt 1475–1588

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6gbd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gbd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6gbd
Deposition date deposition_date2018-04-13
Structure title titleMurine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain
Keywords keywordsPTPN13, PDZ3, protein binding; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.30 Å
Radius of gyration Rg (electron density) rg_electron15.69 Å
Forward intensity I(0) i0857429000.00
Molecular weight molecular_weight253170.0 kDa
Excluded volume excluded_volume319460 ų
Envelope volume envelope_volume45515 ų
Hydration-shell volume shell_volume19490 ų
Envelope diameter envelope_diameter72.8 Å
Shell Rg shell_rg26.29 Å
Envelope Rg envelope_rg20.91 Å
Shape Rg shape_rg15.70 Å
Total Rg total_rg15.89 Å
Total atoms total_atoms35960
Residues n_residues2380
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.2 Å
Rg (real space) rg_real16.30 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real8.5740e+08
I(0) uncertainty (real space) i0_real_error1.0370e+07
Rg (reciprocal space) rg_reciprocal16.30 Å
I(0) (reciprocal space) i0_reciprocal857400000.0000
Solution quality estimate total_estimate0.7524
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.7 Å
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.096
Angular range angular_range— – 0.4900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha395200.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.602; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6gbda1
Class classb — All beta proteins
Fold Fold foldb.36 — PDZ domain-like
Superfamily Superfamily superfamilyb.36.1 — PDZ domain-like
Family Family familyb.36.1.0 — automated matches
Domain ID domain_idd6gbda2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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8. Citations (1)

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9. Files and Curves (10)