SAXSdb — 4rof

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

E3 ubiquitin-protein ligase Itchy homolog

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 436–474	Fragment：UNP residues 436-474	Thioredoxin-interacting protein × 1 （Q9H3M7）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 436–474	Fragment：UNP residues 436-474	Thioredoxin-interacting protein × 1 （Q9H3M7）	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

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 4ROF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DMV Solution structure of the second ww domain of Itchy homolog E3 ubiquitin protein ligase (Itch) Deposited 2006-04-24	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 328–357（30 aa） Fragment：WW domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.4mM protein U-15N, 13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O \| 90% H2O/10% D2O	Resolution not provided
2KYK The sandwich region between two LMP2A PY motif regulates the interaction between AIP4WW2domain and PY motif Deposited 2010-05-28	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 359–392（34 aa） Fragment：WW 2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Pressure ambient NMR sample composition 0.01% [U-95% 13C; U-95% 15N] sodium phosphate-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NQ3 Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase Deposited 2006-10-30	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 1–155（155 aa） Fragment：C2 Domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；The protein at 20 mg/ml was dissolved in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol, 2 mM DTT, and mixed 1:1 with well solution that was 20% PEG3350, 0.1 M bis-Tris, pH 6.0, 0.2 M NH4OAc, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.195
2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 246–270（25 aa） Fragment：AIP4 (209-224)	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 246–270（25 aa） Fragment：AIP4 (209-224)	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
2YSF Solution structure of the fourth WW domain from the human E3 ubiquitin-protein ligase Itchy homolog, ITCH Deposited 2007-04-03	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 480–512（33 aa） Fragment：WW domain, UNP residues 480-512	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 0.9mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3TUG Crystal structure of the HECT domain of ITCH E3 ubiquitin ligase Deposited 2011-09-16	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 524–903（380 aa）	Not recorded	CL CHLORIDE ION × 1 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；30% PEG1500, 0.2M NaCl 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.27 Å R-free 0.256
5C7M CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT Deposited 2015-06-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 524–899（376 aa） Fragment：HECT DOMAIN (UNP RESIDUES 524-899)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml. The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant	Resolution 3.03 Å R-free 0.297
5CQ2 Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide Deposited 2015-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 282–370（89 aa） Fragment：UNP residues 282-370	Not recorded	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
5DWS Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide Deposited 2015-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 285–323（39 aa） Fragment：UNP residues 285-323 Chain C 285–323（39 aa） Fragment：UNP residues 285-323 Chain E 285–323（39 aa） Fragment：UNP residues 285-323 Chain G 285–323（39 aa） Fragment：UNP residues 285-323	Not recorded	UNX UNKNOWN LIGAND × 26	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG-3350, 0.2 M sodium acetate	Resolution 1.65 Å R-free 0.257
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 A 324–363（40 aa） Fragment：UNP residues 324-363 Chain B 324–363（40 aa） Fragment：UNP residues 324-363	Not recorded	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
5SXP STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX Deposited 2016-08-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 249–269（21 aa） Fragment：UNP residues 249-269	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MIB buffer pH 5.0 and 25% PEG1500	Resolution 1.65 Å R-free 0.161
5SXP STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX Deposited 2016-08-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 249–269（21 aa） Fragment：UNP residues 249-269	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MIB buffer pH 5.0 and 25% PEG1500	Resolution 1.65 Å R-free 0.161

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

View Construct and Data Evidence

UniProt name	ITCH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–47； UniProt 436–474 Author chain B； PDBConstruct 9–47； UniProt 436–474

Thioredoxin-interacting protein

OrganismNot specified

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 327–338	Fragment：UNP residues 327-338 Non-standard monomer：Yes (specific site not provided by mmCIF)	E3 ubiquitin-protein ligase Itchy homolog × 1 （Q96J02）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 327–338	Fragment：UNP residues 327-338 Non-standard monomer：Yes (specific site not provided by mmCIF)	E3 ubiquitin-protein ligase Itchy homolog × 1 （Q96J02）	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

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 4ROF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GEI N-terminal domain of VDUP-1 Deposited 2012-08-02	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 2–149（148 aa） Fragment：N-terminal domain, UNP residues 2-149	Mutation：K64A, C36S, C49S, C120S	No recorded non-water small molecule	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
4GEJ N-terminal domain of VDUP-1 Deposited 2012-08-02	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 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 construct Different mutation/modification Different oligomeric state 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 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 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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
4ROJ Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide Deposited 2014-10-28	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 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 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 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TXNIP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–13； UniProt 327–338 Author chain D； PDBConstruct 2–13； UniProt 327–338

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	4rof
Deposition date deposition_date	2014-10-28
Structure title title	Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide
Keywords keywords	Structural Genomics, Structural GenomicsConsortium, SGC, LIGASE, Structural Genomics Consortium; LIGASE
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	16.07 Å
Radius of gyration Rg (electron density) rg_electron	15.40 Å
Forward intensity I(0) i0	2500010.00
Molecular weight molecular_weight	10540.0 kDa
Excluded volume excluded_volume	12936 Å³
Envelope volume envelope_volume	15861 Å³
Hydration-shell volume shell_volume	9476 Å³
Envelope diameter envelope_diameter	59.4 Å
Shell Rg shell_rg	19.74 Å
Envelope Rg envelope_rg	15.62 Å
Shape Rg shape_rg	15.41 Å
Total Rg total_rg	16.25 Å
Total atoms total_atoms	744
Residues n_residues	92
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	58.6 Å
Rg (real space) rg_real	16.15 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	2.5000e+06
I(0) uncertainty (real space) i0_real_error	3.0280e+04
Rg (reciprocal space) rg_reciprocal	16.14 Å
I(0) (reciprocal space) i0_reciprocal	2500000.0000
Solution quality estimate total_estimate	0.6141
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.442
Kurtosis Kurtosis kurtosis	-0.207
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	569500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.677; Smooth: 0.000

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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	E3 ubiquitin-protein ligase Itchy homolog
Molecular weight formula_weight	5412.0 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	768

GRRASVELPLGPLPPGWEKRTDSNGRVYFVNHNTRITQWEDPRSQGQ

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	Thioredoxin-interacting protein
Molecular weight formula_weight	1359.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

XTPEAPPCYMDVIX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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8. Citations (1)

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Unit-cell length a length_a	30.171 Å
Unit-cell length b length_b	55.312 Å
Unit-cell length c length_c	59.796 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2463
R_work r_work	0.2389
R_free r_free	0.2975

fit	/app/data/saxs_computation/ro/4rof/4rof.fit
pddf	/app/data/pr_computation/ro/4rof/4rof.pr.out
profile	/app/data/saxs_computation/ro/4rof/4rof.dat

Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide

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

E3 ubiquitin-protein ligase Itchy homolog

State in the Current Structure

Other States of the Same Protein in the Database

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)