SAXSdb — 2lnw

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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 A； UniProt 659–771	Fragment：UNP RESIDUES 659-771	Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 × 1 （Q8WWN8）	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

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 2LNW	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 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
2DM1 Solution structure of the second SH3 domain of human protein vav-2 Deposited 2006-04-20	Different construct Different oligomeric state Different experimental conditions	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
2LNX Solution structure of Vav2 SH2 domain Deposited 2012-01-05	Different oligomeric state 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 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 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 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 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 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 10–122； UniProt 659–771

Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3

OrganismNot specified

UniProt Q8WWN8

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 B； UniProt 1404–1412	Fragment：UNP RESIDUES 1404-1412 Non-standard monomer：Yes (specific site not provided by mmCIF)	Guanine nucleotide exchange factor VAV2 × 1 （P52735）	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

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 2LNW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KG5 NMR Solution structure of ARAP3-SAM Deposited 2009-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–80（80 aa） Fragment：SAM Domain, residues 1-80	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.7；298 K；Pressure ambient NMR sample composition 1 mM protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-100% 15N] protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein, 2.7 mM potassium chloride, 137 mM sodium chloride, 11.9 mM phosphates, 0.3% mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
5JCP RhoGAP domain of ARAP3 in complex with RhoA in the transition state Deposited 2016-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 906–1107（202 aa） Fragment：UNP residues 906-1107,UNP residues 2-181	Mutation：F25N	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 15%(v/v) PEG 550 MME, 4%(v/v) Acetone	Resolution 2.10 Å R-free 0.227
5JCP RhoGAP domain of ARAP3 in complex with RhoA in the transition state Deposited 2016-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 906–1107（202 aa） Fragment：UNP residues 906-1107,UNP residues 2-181	Mutation：F25N	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 15%(v/v) PEG 550 MME, 4%(v/v) Acetone	Resolution 2.10 Å R-free 0.227
5JD0 crystal structure of ARAP3 RhoGAP domain Deposited 2016-04-15	Different construct Different mutation/modification 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 906–1107（202 aa） Fragment：UNP residues 906-1107	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；100 mM HEPES, 10% PEG8000	Resolution 2.30 Å R-free 0.260
5JD0 crystal structure of ARAP3 RhoGAP domain Deposited 2016-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 906–1107（202 aa） Fragment：UNP residues 906-1107	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；100 mM HEPES, 10% PEG8000	Resolution 2.30 Å R-free 0.260
7A9B Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide Deposited 2020-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1414–1429（16 aa） Chain B 1414–1429（16 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 nL of protein solution (15 mg/ml mutant protein in 10 mM HEPES buffer, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP) were mixed with 100 nL reservoir buffer (16% (w/v) polyethylene glycol 3350 and 0.2 M ammonium citrate), above a reservoir volume of 20 microL	Resolution 2.00 Å R-free 0.249
7YIR Crystal structure of N-terminal PH domain of ARAP3 protein from human Deposited 2022-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–385（102 aa） Fragment：PH1 domain	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS (pH 6.5), 30% v/v Polyethylene glycol monomethyl ether 550	Resolution 2.10 Å R-free 0.230
7YIS Crystal structure of N-terminal PH domain of ARAP3 protein in complex with inositol 1,3,4,5-tetrakisphosphate Deposited 2022-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–385（102 aa） Fragment：PH1 domain	Not recorded	4PT (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% v/v Polyethylene glycol 400	Resolution 3.30 Å R-free 0.276

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

View Construct and Data Evidence

UniProt name	ARAP3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–9； UniProt 1404–1412

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	2lnw
Deposition date deposition_date	2012-01-05
Structure title title	Identification and structural basis for a novel interaction between Vav2 and Arap3
Keywords keywords	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	15.36 Å
Radius of gyration Rg (electron density) rg_electron	14.68 Å
Forward intensity I(0) i0	1192320000.00
Molecular weight molecular_weight	291710.0 kDa
Excluded volume excluded_volume	364020 Å³
Envelope volume envelope_volume	45083 Å³
Hydration-shell volume shell_volume	19741 Å³
Envelope diameter envelope_diameter	64.8 Å
Shell Rg shell_rg	26.05 Å
Envelope Rg envelope_rg	20.27 Å
Shape Rg shape_rg	14.64 Å
Total Rg total_rg	15.03 Å
Total atoms total_atoms	40540
Residues n_residues	2420
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	58.7 Å
Rg (real space) rg_real	15.33 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.1920e+09
I(0) uncertainty (real space) i0_real_error	1.3330e+07
Rg (reciprocal space) rg_reciprocal	15.33 Å
I(0) (reciprocal space) i0_reciprocal	1192000000.0000
Solution quality estimate total_estimate	0.7843
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	0.326
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	666800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.428; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Guanine nucleotide exchange factor VAV2
Molecular weight formula_weight	14628.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	40540

MGHHHHHHMSRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQCHSLKESFKQLDTTLKYPYKSRE

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	Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Molecular weight formula_weight	1130.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EEPVYEEVG

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2lnwA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (1)

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fit	/app/data/saxs_computation/ln/2lnw/2lnw.fit
pddf	/app/data/pr_computation/ln/2lnw/2lnw.pr.out
profile	/app/data/saxs_computation/ln/2lnw/2lnw.dat

Identification and structural basis for a novel interaction between Vav2 and Arap3

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

Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)