4gej

N-terminal domain of VDUP-1

Method: X-RAY DIFFRACTION Dmax: 126.6 Å Quality: REASONABLE

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

Thioredoxin-interacting protein

Homo sapiens

UniProt Q9H3M7

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: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
10 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain J; UniProt 2–149 Fragment:N-terminal domain, UNP residues 2-149 Mutation:C36S, C49S, C120S No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–149 Fragment:N-terminal domain, UNP residues 2-149 Mutation:C36S, C49S, C120S No other associated polymer 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 2–149 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 2–149 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 2–149 Fragment:N-terminal domain, UNP residues 2-149 Mutation:C36S, C49S, C120S No other associated polymer 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
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 2–149 Fragment:N-terminal domain, UNP residues 2-149 Mutation:C36S, C49S, C120S No other associated polymer 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
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 2–149 Fragment:N-terminal domain, UNP residues 2-149 Mutation:C36S, C49S, C120S No other associated polymer 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
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 2–149 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
9 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain I; UniProt 2–149 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

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.

8 other PDB entries and 11 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 Author chain B; PDBConstruct 3–150; UniProt 2–149 Author chain C; PDBConstruct 3–150; UniProt 2–149 Author chain D; PDBConstruct 3–150; UniProt 2–149 Author chain E; PDBConstruct 3–150; UniProt 2–149 Author chain F; PDBConstruct 3–150; UniProt 2–149 Author chain G; PDBConstruct 3–150; UniProt 2–149 Author chain H; PDBConstruct 3–150; UniProt 2–149 Author chain I; PDBConstruct 3–150; UniProt 2–149 Author chain J; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 4gej

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gej
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gej
Deposition date deposition_date2012-08-02
Structure title titleN-terminal domain of VDUP-1
Keywords keywordsalpha-arrestin, oxidative stress, metabolism, thioredoxin, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.23
Radius of gyration Rg (electron density) rg_electron40.52
Forward intensity I(0) i0345401000.00
Molecular weight molecular_weight155230.0 kDa
Excluded volume excluded_volume196020 ų
Envelope volume envelope_volume302460 ų
Hydration-shell volume shell_volume61982 ų
Envelope diameter envelope_diameter138.3
Shell Rg shell_rg46.78
Envelope Rg envelope_rg39.11
Shape Rg shape_rg40.49
Total Rg total_rg41.03
Total atoms total_atoms10938
Residues n_residues1361
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax126.6
Rg (real space) rg_real40.98
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real3.4540e+08
I(0) uncertainty (real space) i0_real_error5.5730e+06
Rg (reciprocal space) rg_reciprocal41.23
I(0) (reciprocal space) i0_reciprocal345500000.0000
Solution quality estimate total_estimate0.6698
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.3
Skewness Skewness skewness0.014
Kurtosis Kurtosis kurtosis-0.501
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19230000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.965; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id4gejA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640
Domain ID domain_id4gejJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640

8. Citations (1)

9. Files and Curves (10)