SAXSdb — 2dm1

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

Protein vav-2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 819–878	Fragment：sh3 domain	No other associated polymer	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

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 2DM1	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 experimental conditions	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
2LNW Identification and structural basis for a novel interaction between Vav2 and Arap3 Deposited 2012-01-05	Different construct Different oligomeric state Different experimental conditions	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 experimental conditions	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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 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
7WFY Crystal Structure of the VAV2 SH2 domain in complex with APP phosphorylated peptide Deposited 2021-12-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 659–771（113 aa）	Not recorded	No recorded non-water small molecule	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

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 A； PDBConstruct 8–67； UniProt 819–878

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	2dm1
Deposition date deposition_date	2006-04-20
Structure title title	Solution structure of the second SH3 domain of human protein vav-2
Keywords keywords	;Rho family Guanine nucleotide exchange factor, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN ;; SIGNALING PROTEIN
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	13.77 Å
Radius of gyration Rg (electron density) rg_electron	13.16 Å
Forward intensity I(0) i0	407132000.00
Molecular weight molecular_weight	156530.0 kDa
Excluded volume excluded_volume	190250 Å³
Envelope volume envelope_volume	33031 Å³
Hydration-shell volume shell_volume	15628 Å³
Envelope diameter envelope_diameter	60.3 Å
Shell Rg shell_rg	24.34 Å
Envelope Rg envelope_rg	19.47 Å
Shape Rg shape_rg	13.09 Å
Total Rg total_rg	13.71 Å
Total atoms total_atoms	21320
Residues n_residues	1460
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	37.1 Å
Rg (real space) rg_real	12.99 Å
Rg uncertainty (real space) rg_real_error	0.05 Å
I(0) (real space) i0_real	3.8820e+08
I(0) uncertainty (real space) i0_real_error	3.1080e+06
Rg (reciprocal space) rg_reciprocal	13.89 Å
I(0) (reciprocal space) i0_reciprocal	407100000.0000
Solution quality estimate total_estimate	0.6775
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	15.0 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.226
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.2090
Highest regularization parameter α highest_alpha	232300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.957; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; 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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2dm1a1
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.34.2.0 — automated matches

Domain ID domain_id	d2dm1a2
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	d2dm1a3
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 (1 domains)

Domain ID domain_id	2dm1A00
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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Description description	Protein vav-2
Molecular weight formula_weight	7852.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	21320

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

fit	/app/data/saxs_computation/dm/2dm1/2dm1.fit
pddf	/app/data/pr_computation/dm/2dm1/2dm1.pr.out
profile	/app/data/saxs_computation/dm/2dm1/2dm1.dat

Solution structure of the second SH3 domain of human protein vav-2

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

Protein vav-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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)