SAXSdb — 1uec

▼

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

Neutrophil cytosol factor 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 151–340	Fragment：autoinhibited tandem SH3 domain, redidues 151-340	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.82 Å R-free 0.236
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 151–340	Fragment：autoinhibited tandem SH3 domain, redidues 151-340	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.82 Å R-free 0.236

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 1UEC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GD5 SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOX NADPH OXIDASE Deposited 2000-09-14	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–128（128 aa） Fragment：PX DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；293 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition 0.6mM PX domain U-15N,13C; 5mM Na-MES buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 359–390（32 aa） Fragment：TAIL PEPTIDE (RESIDUES 359-390)	Not recorded	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
1KQ6 p47phox PX domain Deposited 2002-01-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–141（141 aa） Fragment：PX domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；PEG 550 DME, glycerol, ammonium sulfate, natrium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.18 Å R-free 0.185
1NG2 Structure of autoinhibited p47phox Deposited 2002-12-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 156–340（185 aa） Fragment：residues 156-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.233
1NG2 Structure of autoinhibited p47phox Deposited 2002-12-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 156–340（185 aa） Fragment：residues 156-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.233
1O7K human p47 PX domain complex with sulphates Deposited 2002-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–123（123 aa） Fragment：PX DOMAIN, RESIDUES 1-123 Chain B 1–123（123 aa） Fragment：PX DOMAIN, RESIDUES 1-123 Chain C 1–123（123 aa） Fragment：PX DOMAIN, RESIDUES 1-123	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；1 M AMMONIUM SULPHATE, 0.1M TRIS PH 8.5, 12% GLYCEROL	Resolution 2.00 Å R-free 0.254
1OV3 Structure of the p22phox-p47phox complex Deposited 2003-03-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–285（130 aa） Fragment：Residues 156-285 Chain B 156–285（130 aa） Fragment：Residues 156-285	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.275
1OV3 Structure of the p22phox-p47phox complex Deposited 2003-03-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 156–285（130 aa） Fragment：Residues 156-285 Chain B 156–285（130 aa） Fragment：Residues 156-285	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.275
1W70 SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox Deposited 2004-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 360–372（13 aa） Fragment：POLYPROLINE MOTIF, RESIDUES 360-372	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA	Resolution 1.46 Å R-free 0.207
1W70 SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox Deposited 2004-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 360–372（13 aa） Fragment：POLYPROLINE MOTIF, RESIDUES 360-372	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 TFA trifluoroacetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA	Resolution 1.46 Å R-free 0.207
1WLP Solution Structure Of The P22Phox-P47Phox Complex Deposited 2004-06-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 151–286（136 aa） Fragment：Tandem SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
7YXW Structure of the p22phox A200G mutant in complex with p47phox peptide Deposited 2022-02-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 156–285（130 aa）	Mutation：A200G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 1.2 M sodium citrate tribasic dihydrate, 1:1 protein:precipitant ratio	Resolution 2.50 Å R-free 0.269
8WEJ Structure of human phagocyte NADPH oxidase in the activated state Deposited 2023-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 1–286（286 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–193； UniProt 151–340

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	1uec
Deposition date deposition_date	2003-05-11
Structure title title	Crystal structure of autoinhibited form of tandem SH3 domain of p47phox
Keywords keywords	NADPH oxidase, p47phox, phagocyte, SH3 domain, autoinhibition, SIGNALING PROTEIN; 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	23.52 Å
Radius of gyration Rg (electron density) rg_electron	23.27 Å
Forward intensity I(0) i0	7536080.00
Molecular weight molecular_weight	19732.0 kDa
Excluded volume excluded_volume	24484 Å³
Envelope volume envelope_volume	34847 Å³
Hydration-shell volume shell_volume	14407 Å³
Envelope diameter envelope_diameter	82.0 Å
Shell Rg shell_rg	26.81 Å
Envelope Rg envelope_rg	23.43 Å
Shape Rg shape_rg	23.26 Å
Total Rg total_rg	23.85 Å
Total atoms total_atoms	1394
Residues n_residues	177
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	82.5 Å
Rg (real space) rg_real	23.83 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	7.5360e+06
I(0) uncertainty (real space) i0_real_error	1.2250e+05
Rg (reciprocal space) rg_reciprocal	23.76 Å
I(0) (reciprocal space) i0_reciprocal	7536000.0000
Solution quality estimate total_estimate	0.7950
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.528
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1043000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.641; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.428; Smooth: 0.981

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ueca1
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

Domain ID domain_id	d1ueca2
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 (2 domains)

Domain ID domain_id	1uecA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	1uecA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

▶

8. Citations (1)

▶

Unit-cell length a length_a	100.217 Å
Unit-cell length b length_b	100.217 Å
Unit-cell length c length_c	44.924 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	40.990 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2360

Description description	Neutrophil cytosol factor 1
Molecular weight formula_weight	22020.7 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	1548

Crystal structure of autoinhibited form of tandem SH3 domain of p47phox

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

Neutrophil cytosol factor 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

fit	/app/data/saxs_computation/ue/1uec/1uec.fit
pddf	/app/data/pr_computation/ue/1uec/1uec.pr.out
profile	/app/data/saxs_computation/ue/1uec/1uec.dat