SAXSdb — 6nfa

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

Proto-oncogene vav

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 170–575	Fragment：UNP residues 170-575	ZN ZINC ION × 2 9K1 (2S)-2-{[3-(4-methylphenyl)imidazo[1,2-a]pyrazin-8-yl]amino}-3-(pyridin-3-yl)propan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；16-22% v/v ethylene glycol, 0.1 M Tris, pH 7.3, 15% w/v PEG8000	Resolution 2.70 Å R-free 0.242

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 6NFA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CRH Solution structure of the SH2 domain of human proto-oncogene protein VAV1 Deposited 2005-05-20	Different construct 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 629–775（147 aa） Fragment：SH2 (residues 1-138)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient NMR sample composition 1.15mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2LCT Solution structure of the Vav1 SH2 domain complexed with a Syk-derived doubly phosphorylated peptide Deposited 2011-05-09	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 664–767（104 aa） Fragment：SH2 domain residues 664-767	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1.1 mM [U-13C; U-15N] protein, 20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 1.1 mM peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MC1 Solution structure of the Vav1 SH2 domain complexed with a Syk-derived singly phosphorylated peptide Deposited 2013-08-13	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 664–767（104 aa） Fragment：SH2 domain (UNP residues 664-767)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1 mM [U-99% 13C; U-99% 15N] protein, 1 mM peptide, 20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2ROR Solution structure of the VAV1 SH2 domain complexed with a tyrosine-phosphorylated peptide from SLP76 Deposited 2008-04-08	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 629–775（147 aa） Fragment：SH2 domain, UNP residues 629-775	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1.08mM [U-13C; U-15N] Proto-oncogene vav; 1.08mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3BJI Structural Basis of Promiscuous Guanine Nucleotide Exchange by the T-Cell Essential Vav1 Deposited 2007-12-04	Different construct 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 189–565（377 aa） Fragment：Vav1 DH/PH/CRD	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；17% PEG-3350, 100 mM HEPES, pH 7.5, 200 mM ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.293
3BJI Structural Basis of Promiscuous Guanine Nucleotide Exchange by the T-Cell Essential Vav1 Deposited 2007-12-04	Different construct 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 189–565（377 aa） Fragment：Vav1 DH/PH/CRD	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；17% PEG-3350, 100 mM HEPES, pH 7.5, 200 mM ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.293
3KY9 Autoinhibited Vav1 Deposited 2009-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–584（583 aa） Fragment：CH-DH-PH-C1 DOMAINS	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.02 M TRIS, 0.05 M NACL, 5% GLYCEROL, 2 mM TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.73 Å R-free 0.271
3KY9 Autoinhibited Vav1 Deposited 2009-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–584（583 aa） Fragment：CH-DH-PH-C1 DOMAINS	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.02 M TRIS, 0.05 M NACL, 5% GLYCEROL, 2 mM TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.73 Å R-free 0.271
6NEW Apo structure of the activated truncation of Vav1 Deposited 2018-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 170–575（406 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；16-22% (v/v) Ethylene Glycol, 0.1M TRIS pH 7.3, and 15% (w/v) Polyethylene Glycol 8000	Resolution 2.50 Å R-free 0.257
6NF1 Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity Deposited 2018-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–575（574 aa）	Not recorded	9JY (2S)-3-[(3S)-1-(ethylsulfonyl)piperidin-3-yl]-2-{[3-(4-methylphenyl)imidazo[1,2-a]pyrazin-8-yl]amino}propan-1-ol × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；16-22% (v/v) Ethylene Glycol, 0.1M TRIS pH 7.3, and 15% (w/v) Polyethylene Glycol 8000.	Resolution 2.60 Å R-free 0.233
9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 782–839（58 aa）	Not recorded	ZN ZINC ION × 1 A1BYX (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8	Resolution 3.40 Å R-free 0.271

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAV_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–421； UniProt 170–575

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	6nfa
Deposition date deposition_date	2018-12-19
Structure title title	Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity
Keywords keywords	GEF, Rac, Vav1, SIGNALING PROTEIN-INHIBITOR complex; SIGNALING PROTEIN/INHIBITOR
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	27.34 Å
Radius of gyration Rg (electron density) rg_electron	26.48 Å
Forward intensity I(0) i0	35677100.00
Molecular weight molecular_weight	45232.0 kDa
Excluded volume excluded_volume	56216 Å³
Envelope volume envelope_volume	72022 Å³
Hydration-shell volume shell_volume	23426 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	32.73 Å
Envelope Rg envelope_rg	26.40 Å
Shape Rg shape_rg	26.47 Å
Total Rg total_rg	27.19 Å
Total atoms total_atoms	3167
Residues n_residues	386
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	84.8 Å
Rg (real space) rg_real	27.35 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	3.5680e+07
I(0) uncertainty (real space) i0_real_error	5.2750e+05
Rg (reciprocal space) rg_reciprocal	27.35 Å
I(0) (reciprocal space) i0_reciprocal	35680000.0000
Solution quality estimate total_estimate	0.9078
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.236
Kurtosis Kurtosis kurtosis	-0.699
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6417000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.929

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Proto-oncogene vav
Molecular weight formula_weight	49679.9 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	3243

MGKHHHHHHENLYFQGDEIYEDLMRSEPVSMPPKMTEYDKRCCCLREIQQTEEKYTDTLGSIQQHFLKPLQRFLKPQDIEIIFINIEDLLRVHTHFLKEMKEALGTPGAANLYQVFIKYKERFLVYGRYCSQVESASKHLDRVAAAREDVQMKLEECSQRANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHTQEAMEKENLRLALDAMRDLAQCVNEVKRDNETLRQITNFQLSIENLDQSLAHYGRPKIDGELKITSVERRSKMDRYAFLLDKALLICKRRGDSYDLKDFVNLHSFQVRDDSSGDRDNKKWSHMFLLIEDQGAQGYELFFKTRELKKKWMEQFEMAISNIYPENATANGHDFQMFSFEETTSCKACQMLLRGTFYQGYRCHRCRASAHKECLGRVPPCGRHGQDFPGTM

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2S)-2-{[3-(4-methylphenyl)imidazo[1,2-a]pyrazin-8-yl]amino}-3-(pyridin-3-yl)propan-1-ol
Molecular weight formula_weight	359.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6nfaA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

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8. Citations (1)

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Unit-cell length a length_a	36.880 Å
Unit-cell length b length_b	67.641 Å
Unit-cell length c length_c	179.544 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	63.300 Å
R factor r_factor	0.1900
R_work r_work	0.1880
R_free r_free	0.2420

fit	/app/data/saxs_computation/nf/6nfa/6nfa.fit
pddf	/app/data/pr_computation/nf/6nfa/6nfa.pr.out
profile	/app/data/saxs_computation/nf/6nfa/6nfa.dat

Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity

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

Proto-oncogene vav

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