SAXSdb — 1e96

▼

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

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1

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 1–192	Mutation：YES	NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203 × 1 （P19878） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 10.5；0.1 M CAPS PH 10.5, 0.2 M LI ACETATE, 0.8 M NAH2PO4, 1.2 M K2HPO4	Resolution 2.40 Å R-free 0.284

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 1E96	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HE1 Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac Deposited 2000-11-18	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 C 1–176（176 aa） Fragment：2-184	Not recorded	NI NICKEL (II) ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；8% PEG 6000, 3MM NICL2, 100 MM TRIS/HCL PH8.5, pH 8.50	Resolution 2.00 Å R-free 0.224
1HE1 Crystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac Deposited 2000-11-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–176（176 aa） Fragment：2-184	Not recorded	NI NICKEL (II) ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；8% PEG 6000, 3MM NICL2, 100 MM TRIS/HCL PH8.5, pH 8.50	Resolution 2.00 Å R-free 0.224
1HH4 Rac1-RhoGDI complex involved in NADPH oxidase activation Deposited 2000-12-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–192（192 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；HANGING DROP AT 20C WITH RESERVOIR: 30% PEG 4000, 100 MM NA CITRATE PH=5.6, 5 MM MGCL2, 200 MM AMMONIUM ACETATE, pH 5.60	Resolution 2.70 Å R-free 0.280
1HH4 Rac1-RhoGDI complex involved in NADPH oxidase activation Deposited 2000-12-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–192（192 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；HANGING DROP AT 20C WITH RESERVOIR: 30% PEG 4000, 100 MM NA CITRATE PH=5.6, 5 MM MGCL2, 200 MM AMMONIUM ACETATE, pH 5.60	Resolution 2.70 Å R-free 0.280

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–192； UniProt 1–192

NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203

HOMO SAPIENS

UniProt P19878

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 1–203	Fragment：YES	RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 × 1 （P15154） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 10.5；0.1 M CAPS PH 10.5, 0.2 M LI ACETATE, 0.8 M NAH2PO4, 1.2 M K2HPO4	Resolution 2.40 Å R-free 0.284

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 1E96	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HH8 The active N-terminal region of p67phox: Structure at 1.8 Angstrom resolution and biochemical characterizations of the A128V mutant implicated in chronic granulomatous disease Deposited 2000-12-21	Different construct 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 1–213（213 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-213	Not recorded	FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；100 MM NA CITRATE PH 4.5, 17% PEG 2K MME, 10% GLYCEROL	Resolution 1.80 Å R-free 0.204
1K4U Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox Deposited 2001-10-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 455–516（62 aa） Fragment：C-TERMINAL SH3 DOMAIN (RESIDUES 455-516)	Mutation：C499S/C514S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure 1 NMR sample composition 0.7mM p67SH3(C) U-15N,13C; 0.77mM p47 tail peptide; 5mM MOPSO buffer; 30 mM d10-DTT; 100mM KCl \| 90% H2O, 10% D2O; 100% D2O NMR sample composition 0.5mM p47 tail peptide U-15N,13C; 0.55mM p67SH3(C); 5mM MOPSO buffer; 30mM d10-DTT; 100mM KCl \| 90% H2O, 10% D2O; 100% D2O	Resolution not provided
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	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 A 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 352–429（78 aa） Fragment：PB1 DOMAIN, RESIDUES 352-429	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1WM5 Crystal structure of the N-terminal TPR domain (1-203) of p67phox Deposited 2004-07-03	Different construct 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 1–203（203 aa） Fragment：TPR domain	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；ammonium sulfate, HEPES, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.95 Å R-free 0.224
2DMO Refined solution structure of the 1st SH3 domain from human Neutrophil cytosol factor 2 (NCF-2) Deposited 2006-04-22	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 242–297（56 aa） Fragment：SH3 domain	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 1.3mM SH3 domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	NCF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–203； UniProt 1–203

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1e96
Deposition date deposition_date	2000-10-10
Structure title title	Structure of the Rac/p67phox complex
Keywords keywords	SIGNALING PROTEIN, SIGNALLING COMPLEX, GTPASE, NADPH OXIDASE, PROTEIN-PROTEIN COMPLEX, TPR MOTIF; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.53 Å
Radius of gyration Rg (electron density) rg_electron	22.84 Å
Forward intensity I(0) i0	27699300.00
Molecular weight molecular_weight	41607.0 kDa
Excluded volume excluded_volume	52663 Å³
Envelope volume envelope_volume	62799 Å³
Hydration-shell volume shell_volume	23324 Å³
Envelope diameter envelope_diameter	78.7 Å
Shell Rg shell_rg	29.20 Å
Envelope Rg envelope_rg	22.94 Å
Shape Rg shape_rg	22.83 Å
Total Rg total_rg	23.69 Å
Total atoms total_atoms	2921
Residues n_residues	363
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	79.8 Å
Rg (real space) rg_real	23.50 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	2.7700e+07
I(0) uncertainty (real space) i0_real_error	3.8830e+05
Rg (reciprocal space) rg_reciprocal	23.51 Å
I(0) (reciprocal space) i0_reciprocal	27700000.0000
Solution quality estimate total_estimate	0.7221
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.278
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4679000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.959; Smooth: 0.993

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
Molecular weight formula_weight	21429.1 kDa
Mutation mutation	YES
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	2998

PQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGLEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL

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 polymer

Description description	NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203
Molecular weight formula_weight	23490.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSLVEAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLYEPVVIPVGKLFRPNERQVAQLAKKDYLGKAT

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 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1e96a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d1e96a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1e96b_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

CATH v4.4 (2 domains)

Domain ID domain_id	1e96A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1e96B00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	83.220 Å
Unit-cell length b length_b	83.220 Å
Unit-cell length c length_c	138.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2480
R_work r_work	0.2440
R_free r_free	0.2840

fit	/app/data/saxs_computation/e9/1e96/1e96.fit
pddf	/app/data/pr_computation/e9/1e96/1e96.pr.out
profile	/app/data/saxs_computation/e9/1e96/1e96.dat

Structure of the Rac/p67phox complex

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

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1

State in the Current Structure

Other States of the Same Protein in the Database

NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)