SAXSdb — 7wfy

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

Guanine nucleotide exchange factor VAV2

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 659–771	Not recorded	Amyloid beta A4 protein-binding family B member 1 (protein) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.4；289 K；25% PEG 3350, 0.2 M Magnesium chloride hexahydrate, 0.1 M, Tris/HCl, pH 8.4	Resolution 2.45 Å R-free 0.268

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 7WFY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DLZ Solution structure of the SH2 domain of human protein vav-2 Deposited 2006-04-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 663–767（105 aa） Fragment：sh2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.16mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2DM1 Solution structure of the second SH3 domain of human protein vav-2 Deposited 2006-04-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 819–878（60 aa） Fragment：sh3 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 1.07mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LNW Identification and structural basis for a novel interaction between Vav2 and Arap3 Deposited 2012-01-05	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 659–771（113 aa） Fragment：UNP RESIDUES 659-771	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 3 mM entity_2-2, 5 mM potassium phosphate-3, 20 mM sodium phosphate-4, 5 mM DTT-5, 2 mM EDTA-6, 75 mM sodium chloride-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-8, 3 mM entity_2-9, 5 mM potassium phosphate-10, 75 mM sodium chloride-11, 5 mM DTT-12, 2 mM EDTA-13, 20 mM sodium phosphate-14, 100% D2O \| 100% D2O	Resolution not provided
2LNX Solution structure of Vav2 SH2 domain Deposited 2012-01-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 659–771（113 aa） Fragment：UNP RESIDUES 659-771	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；293 K；Ionic strength (raw mmCIF value) 120 NMR sample composition 1 mM [U-13C; U-15N] entity-1, 5 mM DTT-2, 75 mM sodium chloride-3, 5 mM potassium phosphate-4, 20 mM sodium phosphate-5, 1 mM EDTA-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] entity-7, 75 mM sodium chloride-8, 5 mM DTT-9, 5 mM potassium phosphate-10, 20 mM sodium phosphate-11, 1 mM EDTA-12, 100% D2O \| 100% D2O	Resolution not provided
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 667–782（116 aa） Fragment：UNP residues 667-782	Not recorded	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K	Resolution 1.95 Å R-free 0.219
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 667–782（116 aa） Fragment：UNP residues 667-782	Not recorded	UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K	Resolution 1.95 Å R-free 0.219
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 667–782（116 aa） Fragment：UNP residues 667-782	Not recorded	UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K	Resolution 1.95 Å R-free 0.219
7RNV SH2 domain of guanine nucleotide exchange factor Vav2 in complex with an actin peptide with phosphorylated tyrosine 53 Deposited 2021-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 665–774（110 aa） Fragment：SH2 domain (UNP residues 665-774)	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, pH 8.5, 30% PEG4000	Resolution 2.15 Å R-free 0.272

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAV2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 5–117； UniProt 659–771

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	7wfy
Deposition date deposition_date	2021-12-27
Structure title title	Crystal Structure of the VAV2 SH2 domain in complex with APP phosphorylated peptide
Keywords keywords	Complex, PROTEIN BINDING; PROTEIN BINDING
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	14.64 Å
Radius of gyration Rg (electron density) rg_electron	13.00 Å
Forward intensity I(0) i0	3511550.00
Molecular weight molecular_weight	13123.0 kDa
Excluded volume excluded_volume	16375 Å³
Envelope volume envelope_volume	18158 Å³
Hydration-shell volume shell_volume	11719 Å³
Envelope diameter envelope_diameter	42.9 Å
Shell Rg shell_rg	18.98 Å
Envelope Rg envelope_rg	13.30 Å
Shape Rg shape_rg	12.99 Å
Total Rg total_rg	14.33 Å
Total atoms total_atoms	928
Residues n_residues	111
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	45.8 Å
Rg (real space) rg_real	14.52 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	3.5120e+06
I(0) uncertainty (real space) i0_real_error	3.4310e+04
Rg (reciprocal space) rg_reciprocal	14.53 Å
I(0) (reciprocal space) i0_reciprocal	3512000.0000
Solution quality estimate total_estimate	0.8870
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.6 Å
Skewness Skewness skewness	0.030
Kurtosis Kurtosis kurtosis	-0.377
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	797300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 1.000

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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	Guanine nucleotide exchange factor VAV2
Molecular weight formula_weight	13893.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	936

GSHMSRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQCHSLKESFKQLDTTLKYPYKSRE

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	Amyloid beta A4 protein-binding family B member 1 (protein)
Molecular weight formula_weight	1001.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

QNGYENPT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	62.743 Å
Unit-cell length b length_b	109.589 Å
Unit-cell length c length_c	41.369 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	8

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	2.449 Å
Low-resolution limit resolution_low	41.369 Å
R factor r_factor	0.2319
R_work r_work	0.2275
R_free r_free	0.2678

fit	/app/data/saxs_computation/wf/7wfy/7wfy.fit
pddf	/app/data/pr_computation/wf/7wfy/7wfy.pr.out
profile	/app/data/saxs_computation/wf/7wfy/7wfy.dat

Crystal Structure of the VAV2 SH2 domain in complex with APP phosphorylated peptide

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

Guanine nucleotide exchange factor VAV2

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)