1yd8

COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN

Method: X-RAY DIFFRACTION D_max: 102.2 Å Quality: SUSPICIOUS

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

UBIQUIN

OrganismNot specified

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 U； UniProt 1–76	Not recorded	ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å R-free 0.297
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain V； UniProt 1–76	Not recorded	ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 × 1 （Q9NZ52）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 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 1YD8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AAR STRUCTURE OF A DIUBIQUITIN CONJUGATE AND A MODEL FOR INTERACTION WITH UBIQUITIN CONJUGATING ENZYME (E2) Deposited 1992-04-17	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1P3Q Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9 Deposited 2003-04-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；PEG 3350, magnesium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.277
1P3Q Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9 Deposited 2003-04-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain U 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；PEG 3350, magnesium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.277
1V80 Solution structures of ubiquitin at 30 bar and 3 kbar Deposited 2003-12-27	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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.6；293 K；Ionic strength (raw mmCIF value) 0.03；Pressure 30 NMR measurement conditions pH 4.6；293 K；Ionic strength (raw mmCIF value) 0.03；Pressure 1 NMR sample composition 10mM Ubiquitin; 30mM deutrated acetate buffer; 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 3.0mM 15N-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D20 \| 95% H2O, 5% D20 NMR sample composition 1.8mM 15N-13C-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D2O \| 95% H2O, 5% D20	Resolution not provided
1V81 Solution structures of ubiquitin at 30 bar and 3 kbar Deposited 2003-12-27	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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.6；293 K；Ionic strength (raw mmCIF value) 0.03；Pressure 3000 NMR sample composition 10mM Ubiquitin; 30mM deutrated acetate buffer; 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 3mM 15N-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1.8mM 15N-13C-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WRD Crystal structure of Tom1 GAT domain in complex with ubiquitin Deposited 2004-10-14	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；sodium citrate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.259
1WRD Crystal structure of Tom1 GAT domain in complex with ubiquitin Deposited 2004-10-14	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；sodium citrate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.259
2C7M Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300 NL PLUS 300 NL 20 MG/ML PROTEIN SOLUTION 0.2 M LIS2SO4, 0.1 MES PH 6.5 25% PEG3350	Resolution 2.40 Å R-free 0.214
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2D3G Double sided ubiquitin binding of Hrs-UIM Deposited 2005-09-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；289 K；PEG400, CHES, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.228
2DX5 The complex structure between the mouse EAP45-GLUE domain and ubiquitin Deposited 2006-08-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；18% PEG600, 0.1M HEPPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.35 Å R-free 0.329
2FID Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin Deposited 2005-12-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.268
2FIF Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin Deposited 2005-12-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
2FIF Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin Deposited 2005-12-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
2FIF Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin Deposited 2005-12-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
2OOB crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin Deposited 2007-01-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2M calcium chloride, 0.1M sodium acetate, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.256
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2WWZ TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.202
2WX0 TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.236
2WX0 TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.236
2WX1 TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked tri-ubiquitin, P212121 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.269
3H1U Structure of ubiquitin in complex with Cd ions Deposited 2009-04-14	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 1–76（76 aa）	Not recorded	CD CADMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291.15 K；100mM HEPES pH 7.5, 50mm Cadmium sulfate, 1.0M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 3.00 Å R-free 0.257
3H1U Structure of ubiquitin in complex with Cd ions Deposited 2009-04-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Not recorded	CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291.15 K；100mM HEPES pH 7.5, 50mm Cadmium sulfate, 1.0M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 3.00 Å R-free 0.257
3M3J A new crystal form of Lys48-linked diubiquitin Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；30% PEG 4000, 0.2M lithium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.229
3M3J A new crystal form of Lys48-linked diubiquitin Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；30% PEG 4000, 0.2M lithium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.229
3M3J A new crystal form of Lys48-linked diubiquitin Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；30% PEG 4000, 0.2M lithium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.229

19 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain U； PDBConstruct 1–76； UniProt 1–76 Author chain V； PDBConstruct 1–76； UniProt 1–76

ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3

Homo sapiens

UniProt Q9NZ52

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 H； UniProt 208–301	Not recorded	UBIQUIN × 1 （P62990）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å R-free 0.297
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 208–301	Not recorded	UBIQUIN × 1 （P62990）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å R-free 0.297

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1YD8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	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) 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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	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) 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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	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) 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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	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) 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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JPL GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor Deposited 2001-08-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 10.6；293 K；1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.257
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；293 K；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；293 K；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；293 K；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–166（166 aa） Fragment：VHS domain	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, HANGING DROP；293 K；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	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) 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, HANGING DROP；293 K；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.254
1JUQ GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor Deposited 2001-08-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–166（166 aa） Fragment：VHS domain Chain B 1–166（166 aa） Fragment：VHS domain Chain C 1–166（166 aa） Fragment：VHS domain Chain D 1–166（166 aa） Fragment：VHS domain	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) 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, HANGING DROP；293 K；Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.254
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–166（166 aa） Fragment：VHS domain (residues 1-166)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.255
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–166（166 aa） Fragment：VHS domain (residues 1-166)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.255
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–166（166 aa） Fragment：VHS domain (residues 1-166)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.255
1LF8 Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide Deposited 2002-04-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–166（166 aa） Fragment：VHS domain (residues 1-166)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.255
1P4U CRYSTAL STRUCTURE OF GGA3 GAE DOMAIN IN COMPLEX WITH RABAPTIN-5 PEPTIDE Deposited 2003-04-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 571–723（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M sodium citrate, pH 6.5	Resolution 2.20 Å R-free 0.255
1P4U CRYSTAL STRUCTURE OF GGA3 GAE DOMAIN IN COMPLEX WITH RABAPTIN-5 PEPTIDE Deposited 2003-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 571–723（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.6M sodium citrate, pH 6.5	Resolution 2.20 Å R-free 0.255
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)	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, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)	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, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)	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, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 209–319（111 aa） Fragment：C-GAT domain(RESIDUES 209-319)	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, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290

5 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GGA3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 5–98； UniProt 208–301 Author chain H； PDBConstruct 5–98； UniProt 208–301

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yd8
Deposition date deposition_date	2004-12-23
Structure title title	COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN
Keywords keywords	TRAFFICKING, POST TRANSLATIONAL MODIFICATION, MONO-UBIQUITINATION, PROTEIN TRANSPORT;, PROTEIN TRANSPORT, CHROMOSOMAL PROTEIN; PROTEIN TRANSPORT, CHROMOSOMAL PROTEIN
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	32.99 Å
Radius of gyration Rg (electron density) rg_electron	33.26 Å
Forward intensity I(0) i0	24506400.00
Molecular weight molecular_weight	37937.0 kDa
Excluded volume excluded_volume	47254 Å³
Envelope volume envelope_volume	66738 Å³
Hydration-shell volume shell_volume	18712 Å³
Envelope diameter envelope_diameter	107.2 Å
Shell Rg shell_rg	35.84 Å
Envelope Rg envelope_rg	32.31 Å
Shape Rg shape_rg	33.27 Å
Total Rg total_rg	33.49 Å
Total atoms total_atoms	2662
Residues n_residues	332
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	102.2 Å
Rg (real space) rg_real	33.52 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	2.4510e+07
I(0) uncertainty (real space) i0_real_error	3.9750e+05
Rg (reciprocal space) rg_reciprocal	33.31 Å
I(0) (reciprocal space) i0_reciprocal	24500000.0000
Solution quality estimate total_estimate	0.4858
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.411
Kurtosis Kurtosis kurtosis	-0.846
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1604000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.607; Stabil: 0.998; Sysdev: 0.049; Positv: 1.000; Valcen: 0.327; Smooth: 0.021

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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	UBIQUIN
Molecular weight formula_weight	8576.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V
Atom count atom_count	2808

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity 2 Entity 2 polymer

Description description	ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
Molecular weight formula_weight	11215.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

GAMGIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQV

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1yd8g1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.8 — GAT-like domain
Family Family family	a.7.8.1 — GAT domain

Domain ID domain_id	d1yd8g2
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	d1yd8h2
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.8 — GAT-like domain
Family Family family	a.7.8.1 — GAT domain

Domain ID domain_id	d1yd8h3
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	d1yd8u_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d1yd8v_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (4 domains)

Domain ID domain_id	1yd8G00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	1yd8H00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	1yd8U00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	1yd8V00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	47.886 Å
Unit-cell length b length_b	97.293 Å
Unit-cell length c length_c	66.459 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	26.850 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2970

fit	/app/data/saxs_computation/yd/1yd8/1yd8.fit
pddf	/app/data/pr_computation/yd/1yd8/1yd8.pr.out
profile	/app/data/saxs_computation/yd/1yd8/1yd8.dat

COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN

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

UBIQUIN

State in the Current Structure

Other States of the Same Protein in the Database

ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3

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

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)