SAXSdb — 2mc1

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 664–767	Fragment：SH2 domain (UNP residues 664-767)	Tyrosine-protein kinase SYK × 1 （P48025）	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

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 2MC1	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 oligomeric state Different experimental conditions	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 experimental conditions	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
2ROR Solution structure of the VAV1 SH2 domain complexed with a tyrosine-phosphorylated peptide from SLP76 Deposited 2008-04-08	Different construct Different experimental conditions	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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 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 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
6NFA Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity Deposited 2018-12-19	Different construct 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 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 method 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 4–107； UniProt 664–767

Tyrosine-protein kinase SYK

OrganismNot specified

UniProt P48025

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 338–350	Fragment：UNP residues 338-350 Non-standard monomer：Yes (specific site not provided by mmCIF)	Proto-oncogene vav × 1 （P15498）	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

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 2MC1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LCT Solution structure of the Vav1 SH2 domain complexed with a Syk-derived doubly phosphorylated peptide Deposited 2011-05-09	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 338–350（13 aa） Fragment：sequence database residues 338-350	Non-standard monomer：Yes (specific site not provided by mmCIF)	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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KSYK_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 338–350

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	2mc1
Deposition date deposition_date	2013-08-13
Structure title title	Solution structure of the Vav1 SH2 domain complexed with a Syk-derived singly phosphorylated peptide
Keywords keywords	;SYK KINASE, TYROSINE KINASE, PHOSPHORYLATED PEPTIDE, PHOSPHOTYROSINE BINDING DOMAIN, B CELL SIGNALING PROTEIN, SIGNALING PROTEIN-PROTEIN BINDING complex ;; SIGNALING PROTEIN/PROTEIN BINDING
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	13.56 Å
Radius of gyration Rg (electron density) rg_electron	13.05 Å
Forward intensity I(0) i0	1070410000.00
Molecular weight molecular_weight	278170.0 kDa
Excluded volume excluded_volume	347740 Å³
Envelope volume envelope_volume	26990 Å³
Hydration-shell volume shell_volume	14845 Å³
Envelope diameter envelope_diameter	48.5 Å
Shell Rg shell_rg	21.31 Å
Envelope Rg envelope_rg	15.47 Å
Shape Rg shape_rg	13.02 Å
Total Rg total_rg	13.31 Å
Total atoms total_atoms	38740
Residues n_residues	2380
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	51.3 Å
Rg (real space) rg_real	13.44 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.0700e+09
I(0) uncertainty (real space) i0_real_error	1.3500e+07
Rg (reciprocal space) rg_reciprocal	13.45 Å
I(0) (reciprocal space) i0_reciprocal	1070000000.0000
Solution quality estimate total_estimate	0.7122
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	-0.024
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	477800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.427; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2mc1A01
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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Description description	Proto-oncogene vav
Molecular weight formula_weight	12335.1 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	38740

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

Description description	Tyrosine-protein kinase SYK
Molecular weight formula_weight	1594.5 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/mc/2mc1/2mc1.fit
pddf	/app/data/pr_computation/mc/2mc1/2mc1.pr.out
profile	/app/data/saxs_computation/mc/2mc1/2mc1.dat

Solution structure of the Vav1 SH2 domain complexed with a Syk-derived singly phosphorylated peptide

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

Tyrosine-protein kinase SYK

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)