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1f5x

NMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN

Method: SOLUTION NMR Dmax: 64.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RHO-GEF VAV

Mus musculus

UniProt P27870

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 168–375 Fragment：DBL HOMOLOGY DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR sample composition：1.4 mM 15N,13C,2H; 20 mM phosphate buffer; 50 mM NaCl; 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 1F5X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GCP CRYSTAL STRUCTURE OF VAV SH3 DOMAIN Deposited 2000-08-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 595–660（66 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K
Resolution 2.10 Å R-free 0.253
1GCP CRYSTAL STRUCTURE OF VAV SH3 DOMAIN Deposited 2000-08-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 595–660（66 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K
Resolution 2.10 Å R-free 0.253
1GCP CRYSTAL STRUCTURE OF VAV SH3 DOMAIN Deposited 2000-08-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 595–660（66 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K
Resolution 2.10 Å R-free 0.253
1GCP CRYSTAL STRUCTURE OF VAV SH3 DOMAIN Deposited 2000-08-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 595–660（66 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.2 K；PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K
Resolution 2.10 Å R-free 0.253
1GCQ CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS Deposited 2000-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 595–660（66 aa） Fragment：N-TERMINAL SH3 DOMAIN
Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.2 K；2-methyl-2,4-pentanediol, imidazole, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K
Resolution 1.68 Å R-free 0.235
1K1Z Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav Deposited 2001-09-26 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 583–660（78 aa） Fragment：N-terminal SH3 domain
Mutation：P33G No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Pressure 1
NMR sample composition 1.5mM protein U-15N,13C; 10mM phosphate buffer K; 10mM DTT-d | 90% H2O/10% D2O
Resolution not provided
2KBT Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method Deposited 2008-12-07 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 784–844（61 aa） Fragment：SH3 2 domain of Proto-oncogene vav,UNP residues 228-282 of Immunoglobulin G-binding protein G
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 20 mM MES-1, 2 mM DTT-2, 150 mM NaCl-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2VRW Critical structural role for the PH and C1 domains of the Vav1 exchange factor Deposited 2008-04-16 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 B 170–575（406 aa） Fragment：RESIDUES 170-575
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；100MM BICINE PH9.0 10% PEG 6000
Resolution 1.85 Å R-free 0.251

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

View Construct and Data Evidence
UniProt name VAV_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–208； UniProt 168–375

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 1f5x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1f5x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1f5x
Deposition date deposition_date2000-06-18
Structure title titleNMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN
Keywords keywords11 alpha-HELICES, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.00 Å
Radius of gyration Rg (electron density) rg_electron18.61 Å
Forward intensity I(0) i03351590000.00
Molecular weight molecular_weight489050.0 kDa
Excluded volume excluded_volume611060 ų
Envelope volume envelope_volume58425 ų
Hydration-shell volume shell_volume23346 ų
Envelope diameter envelope_diameter69.7 Å
Shell Rg shell_rg27.81 Å
Envelope Rg envelope_rg21.15 Å
Shape Rg shape_rg18.57 Å
Total Rg total_rg18.86 Å
Total atoms total_atoms68800
Residues n_residues4160
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 dmax64.4 Å
Rg (real space) rg_real19.01 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.3520e+09
I(0) uncertainty (real space) i0_real_error4.7750e+07
Rg (reciprocal space) rg_reciprocal19.01 Å
I(0) (reciprocal space) i0_reciprocal3352000000.0000
Solution quality estimate total_estimate0.8700
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.6 Å
Skewness Skewness skewness0.384
Kurtosis Kurtosis kurtosis-0.233
Angular range angular_range— – 0.4200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1766000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.992
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1f5xa_
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)

CATH v4.4 (1 domains)

Domain ID domain_id1f5xA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
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8. Citations (1)

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9. Files and Curves (10)