SAXSdb — 2d0n

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

GRB2-related adaptor protein 2

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 267–322 Chain C； UniProt 267–322	Fragment：C-terminal SH3 domain	SLP-76 binding peptide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.26M ammonium sulfate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.57 Å R-free 0.284

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 2D0N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H3H Structural Basis for Specific Recognition of an RxxK-containing SLP-76 peptide by the Gads C-terminal SH3 domain Deposited 2002-09-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 263–322（60 aa） Fragment：C-TERMINAL SH3 DOMAIN, RESIDUES 263-322	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；285 K；Ionic strength (raw mmCIF value) 100MM NACL, 50MM SODIUM PHOSPHATE；Pressure 1	Resolution not provided
1OEB Mona/Gads SH3C domain Deposited 2003-03-24	Different construct Different mutation/modification 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 265–322（58 aa） Fragment：SH3C DOMAIN, RESIDUES 265-322	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLISED FROM: 20% PEG4000, 5 MM CDCL2,50 MM NA CACODYLATE PH 6.5	Resolution 1.76 Å R-free 0.235
1OEB Mona/Gads SH3C domain Deposited 2003-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 265–322（58 aa） Fragment：SH3C DOMAIN, RESIDUES 265-322	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLISED FROM: 20% PEG4000, 5 MM CDCL2,50 MM NA CACODYLATE PH 6.5	Resolution 1.76 Å R-free 0.235
1R1P Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification 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 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.241
1R1P Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification 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 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.241
1R1P Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.241
1R1P Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.241
1R1Q Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification 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 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.225
1R1Q Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification 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 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.225
1R1Q Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 50–147（98 aa） Fragment：Gads-SH2 domain Chain B 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.225
1R1S Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification 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 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.259
1R1S Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.259
1R1S Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.259
1R1S Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.259
1R1S Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 50–147（98 aa） Fragment：Gads-SH2 domain Chain E 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.259
1R1S Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads Deposited 2003-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 50–147（98 aa） Fragment：Gads-SH2 domain Chain G 50–147（98 aa） Fragment：Gads-SH2 domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.259
1UTI Mona/Gads SH3C in complex with HPK derived peptide Deposited 2003-12-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 265–322（58 aa） Fragment：SH3C DOMAIN, RESIDUES 265-322	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE, 0.05M HEPES PH7.5, pH 7.50	Resolution 1.50 Å R-free 0.221
2W10 Mona SH3C in complex Deposited 2008-10-13	Different construct Different mutation/modification 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 265–322（58 aa） Fragment：SH3 2, RESIDUES 265-322	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M PHOSPHATE CITRATE, 2 M AMMONIUM SULPHATE, pH 7.5	Resolution 1.90 Å R-free 0.231
2W10 Mona SH3C in complex Deposited 2008-10-13	Different construct Different mutation/modification 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 265–322（58 aa） Fragment：SH3 2, RESIDUES 265-322	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M PHOSPHATE CITRATE, 2 M AMMONIUM SULPHATE, pH 7.5	Resolution 1.90 Å R-free 0.231

7 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GRAP2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–59； UniProt 267–322 Author chain C； PDBConstruct 4–59； UniProt 267–322

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	2d0n
Deposition date deposition_date	2005-08-04
Structure title title	Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction
Keywords keywords	SH3 DOMAIN-COMPLEX, MONA/GADS SH3C DOMAIN, 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	15.96 Å
Radius of gyration Rg (electron density) rg_electron	14.95 Å
Forward intensity I(0) i0	4421590.00
Molecular weight molecular_weight	14955.0 kDa
Excluded volume excluded_volume	18651 Å³
Envelope volume envelope_volume	21511 Å³
Hydration-shell volume shell_volume	12468 Å³
Envelope diameter envelope_diameter	50.1 Å
Shell Rg shell_rg	20.22 Å
Envelope Rg envelope_rg	15.25 Å
Shape Rg shape_rg	14.91 Å
Total Rg total_rg	16.10 Å
Total atoms total_atoms	1059
Residues n_residues	133
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	51.4 Å
Rg (real space) rg_real	15.92 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	4.4220e+06
I(0) uncertainty (real space) i0_real_error	4.7260e+04
Rg (reciprocal space) rg_reciprocal	15.92 Å
I(0) (reciprocal space) i0_reciprocal	4422000.0000
Solution quality estimate total_estimate	0.7127
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.8 Å
Skewness Skewness skewness	0.294
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1631000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.999; Smooth: 0.952

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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	GRB2-related adaptor protein 2
Molecular weight formula_weight	6719.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1258

GSPWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMMR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	SLP-76 binding peptide
Molecular weight formula_weight	1002.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

PSIDRSTKP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d0na2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d2d0na3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2d0nc2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d2d0nc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2d0nA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2d0nC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	58.622 Å
Unit-cell length b length_b	58.622 Å
Unit-cell length c length_c	74.098 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	16

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	7.900 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2840

fit	/app/data/saxs_computation/d0/2d0n/2d0n.fit
pddf	/app/data/pr_computation/d0/2d0n/2d0n.pr.out
profile	/app/data/saxs_computation/d0/2d0n/2d0n.dat

Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction

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

GRB2-related adaptor protein 2

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)