SAXSdb — 4gei

▼

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

Thioredoxin-interacting protein

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 2–149	Fragment：N-terminal domain, UNP residues 2-149 Mutation：K64A, C36S, C49S, C120S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：batch；pH 7.15；277 K；25mM Hepes, 1 mM DTT, pH 7.15, batch, temperature 277K	Resolution 1.50 Å R-free 0.203

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 4GEI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	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 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：C36S, C49S, C120S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.294
4GFX Crystal structure of the N-terminal domain of TXNIP Deposited 2012-08-04	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 4–154（151 aa） Fragment：N-terminal domain (UNP residues 4-154)	Mutation：F4V,K5A,K6A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.75 M sodium/potassium phosphate, 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.60 Å R-free 0.227
4LL1 The structure of the TRX and TXNIP complex Deposited 2013-07-09	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 3–317（315 aa） Fragment：UNP residues 3-317 Chain C 3–317（315 aa） Fragment：UNP residues 3-317	Mutation：C120S, C170S, C205S, C267S Mutation：C120S, C170S, C205S, C267S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；0.16M tri-sodium citrate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K	Resolution 2.00 Å R-free 0.288
4LL4 The structure of the TRX and TXNIP complex Deposited 2013-07-09	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 3–317（315 aa） Fragment：UNP residues 3-317 Chain C 3–317（315 aa） Fragment：UNP residues 3-317	Mutation：C170S, C205S, C267S Mutation：C170S, C205S, C267S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；0.16M tri-sodium citrate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K	Resolution 2.70 Å R-free 0.264
4ROF Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide Deposited 2014-10-28	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 C 327–338（12 aa） Fragment：UNP residues 327-338	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, SITTING DROP；293 K；1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, vapor diffusion, sitting drop, temperature 293K	Resolution 2.03 Å R-free 0.297
4ROF Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide Deposited 2014-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 327–338（12 aa） Fragment：UNP residues 327-338	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, SITTING DROP；293 K；1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, vapor diffusion, sitting drop, temperature 293K	Resolution 2.03 Å R-free 0.297
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	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 D 327–338（12 aa） Fragment：UNP residues 327-338	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K	Resolution 1.95 Å R-free 0.219
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	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 E 327–338（12 aa） Fragment：UNP residues 327-338	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K	Resolution 1.95 Å R-free 0.219
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 327–338（12 aa） Fragment：UNP residues 327-338	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K	Resolution 1.95 Å R-free 0.219
5CQ2 Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide Deposited 2015-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 327–338（12 aa） Fragment：UNP Residues 327-338 Chain C 327–338（12 aa） Fragment：UNP Residues 327-338	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 72	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；30% PEG4000, 0.2 M magnesium chloride, 0.1 M TRIS	Resolution 1.40 Å R-free 0.184
5DZD Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide Deposited 2015-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 327–338（12 aa） Fragment：UNP residues 327-338 Chain D 327–338（12 aa） Fragment：UNP residues 327-338	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；2 M sodium formate, 0.1 M Tris, pH 8.5	Resolution 1.57 Å R-free 0.206

8 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TXNIP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–150； UniProt 2–149

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	4gei
Deposition date deposition_date	2012-08-02
Structure title title	N-terminal domain of VDUP-1
Keywords keywords	alpha-arrestin, oxidative stress, metabolism, thioredoxin, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.48 Å
Radius of gyration Rg (electron density) rg_electron	18.57 Å
Forward intensity I(0) i0	4858180.00
Molecular weight molecular_weight	16321.0 kDa
Excluded volume excluded_volume	20587 Å³
Envelope volume envelope_volume	24895 Å³
Hydration-shell volume shell_volume	12665 Å³
Envelope diameter envelope_diameter	70.2 Å
Shell Rg shell_rg	22.85 Å
Envelope Rg envelope_rg	19.03 Å
Shape Rg shape_rg	18.49 Å
Total Rg total_rg	19.58 Å
Total atoms total_atoms	1151
Residues n_residues	144
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	70.2 Å
Rg (real space) rg_real	19.73 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	4.8580e+06
I(0) uncertainty (real space) i0_real_error	7.0680e+04
Rg (reciprocal space) rg_reciprocal	19.69 Å
I(0) (reciprocal space) i0_reciprocal	4858000.0000
Solution quality estimate total_estimate	0.7905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.624
Kurtosis Kurtosis kurtosis	-0.057
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1388000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.596; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.533; Smooth: 0.954

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4geiA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	98.250 Å
Unit-cell length b length_b	76.280 Å
Unit-cell length c length_c	31.030 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.130 Å
R factor r_factor	0.1820
R_work r_work	0.1796
R_free r_free	0.2033

Description description	Thioredoxin-interacting protein
Molecular weight formula_weight	17048.4 kDa
Mutation mutation	K64A, C36S, C49S, C120S
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1538

N-terminal domain of VDUP-1

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

Thioredoxin-interacting protein

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) 1 domains

CATH v4.4 (1 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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

fit	/app/data/saxs_computation/ge/4gei/4gei.fit
pddf	/app/data/pr_computation/ge/4gei/4gei.pr.out
profile	/app/data/saxs_computation/ge/4gei/4gei.dat