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6nf1

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

Method: X-RAY DIFFRACTION Dmax: 83.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proto-oncogene vav

Homo sapiens

UniProt P15498

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 2–575 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

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 6NF1 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
6NFA Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity Deposited 2018-12-19 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） Fragment：UNP residues 170-575
Not recorded 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
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 5–578； UniProt 2–575

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6nf1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6nf1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6nf1
Deposition date deposition_date2018-12-18
Structure title titleVav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity
Keywords keywordsGEF, Rac, Vav1, inhibitor, METAL BINDING PROTEIN-INHIBITOR complex; METAL BINDING PROTEIN/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.02 Å
Radius of gyration Rg (electron density) rg_electron26.87 Å
Forward intensity I(0) i069061400.00
Molecular weight molecular_weight63661.0 kDa
Excluded volume excluded_volume79173 ų
Envelope volume envelope_volume100480 ų
Hydration-shell volume shell_volume30946 ų
Envelope diameter envelope_diameter87.6 Å
Shell Rg shell_rg34.49 Å
Envelope Rg envelope_rg26.64 Å
Shape Rg shape_rg26.86 Å
Total Rg total_rg27.70 Å
Total atoms total_atoms4456
Residues n_residues550
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.8 Å
Rg (real space) rg_real27.86 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real6.9060e+07
I(0) uncertainty (real space) i0_real_error8.9060e+05
Rg (reciprocal space) rg_reciprocal27.91 Å
I(0) (reciprocal space) i0_reciprocal69060000.0000
Solution quality estimate total_estimate0.9145
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.2 Å
Skewness Skewness skewness0.091
Kurtosis Kurtosis kurtosis-0.643
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15870000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6nf1A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
Domain ID domain_id6nf1A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
Domain ID domain_id6nf1A03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id6nf1A04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)