SAXSdb — 1ywo

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

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1

Rattus norvegicus

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 790–851	Mutation：C5S	Lymphocyte cytosolic protein 2 × 1 （Q13094）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；malonate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.81 Å R-free 0.221

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 1YWO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y0M Crystal structure of of the SH3 domain of phospholipase C Gamma-1 Deposited 2004-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 791–851（61 aa） Fragment：SH3 domain: sequence database residues 791-851	Mutation：C794S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.177
1YWP Phospholipase Cgamma1 SH3 Deposited 2005-02-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 790–851（62 aa） Fragment：Phospholipase C-gamma1	Mutation：C5S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；PEG 4000, sodium acetate, Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.60 Å R-free 0.188
2FJL Solution Structure of the Split PH domain in Phospholipase C-gamma1 Deposited 2006-01-03	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 489–547（59 aa） Fragment：the Split PH2 domain, residuse 1-35 and 112-148 Chain A 851–933（83 aa） Fragment：the Split PH2 domain, residuse 1-35 and 112-148	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Pressure ambient NMR sample composition 1.0mM of the PHN-PHC tandem U-15N; 50mM potassium phosphate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0mM of the PHN-PHC tandem U-15N,13C; 50mM potassium phosphate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0mM of the PHN-PHC tandem U-15N,13C; 50mM potassium phosphate; 100% D2O \| 100% D2O NMR sample composition 1.0mM of the PHN-PHC tandem; 50mM potassium phosphate; 100% D2O \| 100% D2O	Resolution not provided
3GQI Crystal Structure of activated receptor tyrosine kinase in complex with substrates Deposited 2009-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 545–770（226 aa） Fragment：tandem SH2 domains	Not recorded	DVT DECAVANADATE × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEg 8000, taurine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.289
4K44 Auto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes Deposited 2013-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 664–766（103 aa） Fragment：C-terminal SH2 (cSH2) domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；100 mM MES, 200 mM ammonium acetate, 25% (w/v) PEG 4.000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.223
4K44 Auto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes Deposited 2013-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 664–766（103 aa） Fragment：C-terminal SH2 (cSH2) domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；100 mM MES, 200 mM ammonium acetate, 25% (w/v) PEG 4.000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.223
4K45 Auto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes Deposited 2013-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 664–766（103 aa） Fragment：C-terminal SH2 (cSH2) domain Chain B 770–787（18 aa） Fragment：residues 770 to 787 of PLC-gamma1	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；100 mM MES, 200 mM ammonium acetate, 35% (w/v) PEG 4,000, microseeding, pH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 1.50 Å R-free 0.198
5EG3 Crystal Structure of the Activated FGF Receptor 2 (FGFR2) Kinase Domain in complex with the cSH2 domain of Phospholipase C gamma (PLCgamma) Deposited 2015-10-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 661–773（113 aa） Fragment：UNP residues 661-773	Not recorded	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；25 mM HEPES (pH 7.5), PEG20000 (12% 18%) and 2% (w/v) Benzamidine hydrochloride	Resolution 2.61 Å R-free 0.237
6PBC Structural basis for the activation of PLC-gamma isozymes by phosphorylation and cancer-associated mutations Deposited 2019-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 791–1215（425 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12.5% w/v PEG 3,350, 50 mM di-sodium tartrate, 5% v/v glycerol	Resolution 2.46 Å R-free 0.245
7Z3J Structure of crystallisable rat Phospholipase C gamma 1 in complex with inositol 1,4,5-trisphosphate Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–790（771 aa） Chain A 791–1215（425 aa）	Not recorded	CA CALCIUM ION × 2 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；18.7 % PEG 3350, 0.1 M CBTP	Resolution 2.00 Å R-free 0.256
9QB7 Structure of rat Phospholipase C gamma 1 mutant S345F Deposited 2025-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–765（765 aa） Chain A 791–1290（500 aa）	Mutation：S345F Mutation：S345F	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；18.7 % PEG 3350, 0.1 M CBTP, PH 7.0	Resolution 2.56 Å R-free 0.233

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

View Construct and Data Evidence

UniProt name	PLCG1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–64； UniProt 790–851

Lymphocyte cytosolic protein 2

OrganismNot specified

UniProt Q13094

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 P； UniProt 185–194	Not recorded	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 × 1 （P10686）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；malonate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.81 Å R-free 0.221

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 1YWO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H3H Structural Basis for Specific Recognition of an RxxK-containing SLP-76 peptide by the Gads C-terminal SH3 domain Deposited 2002-09-03	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 226–235（10 aa） Fragment：RESIDUES 226-235	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；285 K；Ionic strength (raw mmCIF value) 100MM NACL, 50MM SODIUM PHOSPHATE；Pressure 1	Resolution not provided
2EAP Solution structure of the N-terminal SAM-domain of human lymphocyte cytosolic protein 2 Deposited 2007-01-31	Different construct 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 1–83（83 aa） Fragment：N-terminal SAM domain, residues 8-90	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure AMBIENT NMR sample composition 1.16mM SAM DOMAIN; 20mM d-TRIS-HCL; 100mM NaCl; 1mM d-DTT; 0.02 % NaN3; 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 mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 122–136（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LCP2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 185–194

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	1ywo
Deposition date deposition_date	2005-02-18
Structure title title	Phospholipase Cgamma1 SH3 in complex with a SLP-76 motif
Keywords keywords	SH3, Phospholipase C-gamma1, SLP-76, SH2 domain-containing leukocyte phosphoprotein of 76 kD, HYDROLASE, SIGNALING PROTEIN; HYDROLASE, SIGNALING PROTEIN
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	12.40 Å
Radius of gyration Rg (electron density) rg_electron	10.87 Å
Forward intensity I(0) i0	1277090.00
Molecular weight molecular_weight	7559.0 kDa
Excluded volume excluded_volume	9475 Å³
Envelope volume envelope_volume	10365 Å³
Hydration-shell volume shell_volume	8261 Å³
Envelope diameter envelope_diameter	37.1 Å
Shell Rg shell_rg	16.39 Å
Envelope Rg envelope_rg	11.40 Å
Shape Rg shape_rg	10.79 Å
Total Rg total_rg	12.58 Å
Total atoms total_atoms	536
Residues n_residues	65
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	40.0 Å
Rg (real space) rg_real	12.32 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.2770e+06
I(0) uncertainty (real space) i0_real_error	1.2790e+04
Rg (reciprocal space) rg_reciprocal	12.33 Å
I(0) (reciprocal space) i0_reciprocal	1277000.0000
Solution quality estimate total_estimate	0.8797
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.7 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.244
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	428000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1
Molecular weight formula_weight	7414.3 kDa
EC 编号 ec_number	3.1.4.11
Mutation mutation	C5S
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	614

GSPTFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Lymphocyte cytosolic protein 2
Molecular weight formula_weight	1147.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

QPPVPPQRPM

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ywoa_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (1 domains)

Domain ID domain_id	1ywoA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	46.723 Å
Unit-cell length b length_b	46.723 Å
Unit-cell length c length_c	58.112 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	36.420 Å
R factor r_factor	0.1729
R_work r_work	0.1706
R_free r_free	0.2213

fit	/app/data/saxs_computation/yw/1ywo/1ywo.fit
pddf	/app/data/pr_computation/yw/1ywo/1ywo.pr.out
profile	/app/data/saxs_computation/yw/1ywo/1ywo.dat

Phospholipase Cgamma1 SH3 in complex with a SLP-76 motif

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

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1

State in the Current Structure

Other States of the Same Protein in the Database

Lymphocyte cytosolic protein 2

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)