SAXSdb — 1gm1

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

PROTEIN TYROSINE PHOSPHATASE

MUS MUSCULUS

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 1351–1444	Fragment：PDZ2	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.3；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1	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 1GM1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
6GBD Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain Deposited 2018-04-13	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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, 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
6GBE Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex Deposited 2018-04-13	Different construct 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	Q64512
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 1351–1444

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	1gm1
Deposition date deposition_date	2001-09-06
Structure title title	Second PDZ Domain (PDZ2) of PTP-BL
Keywords keywords	PDZ, PTP-BL, FAS INTERACTION, LIM INTERACTION, STRUCTURAL PROTEIN, CYTOSKELETON, HYDROLASE; HYDROLASE
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.06 Å
Radius of gyration Rg (electron density) rg_electron	12.69 Å
Forward intensity I(0) i0	1649840000.00
Molecular weight molecular_weight	341360.0 kDa
Excluded volume excluded_volume	426940 Å³
Envelope volume envelope_volume	25782 Å³
Hydration-shell volume shell_volume	14285 Å³
Envelope diameter envelope_diameter	48.5 Å
Shell Rg shell_rg	21.15 Å
Envelope Rg envelope_rg	15.57 Å
Shape Rg shape_rg	12.67 Å
Total Rg total_rg	12.88 Å
Total atoms total_atoms	48755
Residues n_residues	3290
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	42.1 Å
Rg (real space) rg_real	12.96 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.6500e+09
I(0) uncertainty (real space) i0_real_error	1.8710e+07
Rg (reciprocal space) rg_reciprocal	12.97 Å
I(0) (reciprocal space) i0_reciprocal	1650000000.0000
Solution quality estimate total_estimate	0.7951
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.054
Kurtosis Kurtosis kurtosis	-0.300
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	140300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; 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 (1 domains)

Domain ID domain_id	d1gm1a_
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	1gm1A00
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	PROTEIN TYROSINE PHOSPHATASE
Molecular weight formula_weight	9767.1 kDa
EC 编号 ec_number	3.1.3.48
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	48755

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Second PDZ Domain (PDZ2) of PTP-BL

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

PROTEIN TYROSINE 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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)

fit	/app/data/saxs_computation/gm/1gm1/1gm1.fit
pddf	/app/data/pr_computation/gm/1gm1/1gm1.pr.out
profile	/app/data/saxs_computation/gm/1gm1/1gm1.dat