2c7n

Human Rabex-5 residues 1-74 in complex with Ubiquitin

Method: X-RAY DIFFRACTION D_max: 128.5 Å Quality: GOOD

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

RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1

HOMO SAPIENS

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–74	Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	UBIQUITIN × 1 （P62990） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–74	Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	UBIQUITIN × 1 （P62990） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–74	Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	UBIQUITIN × 1 （P62990） 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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1–74	Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	UBIQUITIN × 1 （P62990） 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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 1–74	Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	UBIQUITIN × 1 （P62990） 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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain K； UniProt 1–74	Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	UBIQUITIN × 1 （P62990） 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

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 2C7N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2C7M Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–74（74 aa） Fragment：TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74	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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q53FG0_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–74； UniProt 1–74 Author chain C； PDBConstruct 1–74； UniProt 1–74 Author chain E； PDBConstruct 1–74； UniProt 1–74 Author chain G； PDBConstruct 1–74； UniProt 1–74 Author chain I； PDBConstruct 1–74； UniProt 1–74 Author chain K； PDBConstruct 1–74； UniProt 1–74

UBIQUITIN

OrganismNot specified

UniProt P62990

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 B； UniProt 1–76	Not recorded	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–76	Not recorded	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1–76	Not recorded	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） 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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–76	Not recorded	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） 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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain J； UniProt 1–76	Not recorded	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） 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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 1–76	Not recorded	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2C7N	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 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	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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	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 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	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 ligand/ion 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
1YD8 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN Deposited 2004-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.297
1YD8 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN Deposited 2004-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.297
2C7M Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	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	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
2D3G Double sided ubiquitin binding of Hrs-UIM Deposited 2005-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 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 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	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 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 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 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 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	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 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	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 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	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 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	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 ligand/ion 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 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	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 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	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 experimental conditions 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 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	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 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76 Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain L； PDBConstruct 1–76； UniProt 1–76

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	2c7n
Deposition date deposition_date	2005-11-25
Structure title title	Human Rabex-5 residues 1-74 in complex with Ubiquitin
Keywords keywords	PROTEIN-BINDING, UBIQUITIN BINDING DOMAIN, ENDOCYTOSIS, NUCLEAR PROTEIN, POLYPROTEIN, UBIQUITIN COMPLEX, PROTEIN BINDING; PROTEIN BINDING
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	39.25 Å
Radius of gyration Rg (electron density) rg_electron	38.73 Å
Forward intensity I(0) i0	125987000.00
Molecular weight molecular_weight	88267.0 kDa
Excluded volume excluded_volume	109850 Å³
Envelope volume envelope_volume	176970 Å³
Hydration-shell volume shell_volume	39605 Å³
Envelope diameter envelope_diameter	131.7 Å
Shell Rg shell_rg	43.38 Å
Envelope Rg envelope_rg	36.77 Å
Shape Rg shape_rg	38.73 Å
Total Rg total_rg	39.07 Å
Total atoms total_atoms	6184
Residues n_residues	765
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	128.5 Å
Rg (real space) rg_real	39.15 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	1.2600e+08
I(0) uncertainty (real space) i0_real_error	1.9590e+06
Rg (reciprocal space) rg_reciprocal	39.21 Å
I(0) (reciprocal space) i0_reciprocal	126000000.0000
Solution quality estimate total_estimate	0.8908
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.8 Å
Skewness Skewness skewness	0.111
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7139000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.876

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1
Molecular weight formula_weight	8784.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	6437

MSLKSERRGIHVDQSDLLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQS

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	UBIQUITIN
Molecular weight formula_weight	8576.8 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

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7. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2c7na1
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

Domain ID domain_id	d2c7nb1
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	d2c7nc1
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

Domain ID domain_id	d2c7nd1
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	d2c7nf1
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	d2c7ng1
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

Domain ID domain_id	d2c7nh1
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	d2c7ni1
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

Domain ID domain_id	d2c7nj1
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	d2c7nl1
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 (12 domains)

Domain ID domain_id	2c7nA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2c7nB00
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	2c7nC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2c7nD00
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	2c7nE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2c7nF00
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	2c7nG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2c7nH00
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	2c7nI01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2c7nJ00
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	2c7nK01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2c7nL00
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	44.300 Å
Unit-cell length b length_b	68.900 Å
Unit-cell length c length_c	98.500 Å
Unit-cell angle α angle_alpha	108.20 °
Unit-cell angle β angle_beta	102.70 °
Unit-cell angle γ angle_gamma	90.40 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1980
R_work r_work	0.1950
R_free r_free	0.2380

fit	/app/data/saxs_computation/c7/2c7n/2c7n.fit
pddf	/app/data/pr_computation/c7/2c7n/2c7n.pr.out
profile	/app/data/saxs_computation/c7/2c7n/2c7n.dat

Human Rabex-5 residues 1-74 in complex with Ubiquitin

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

RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1

State in the Current Structure

Other States of the Same Protein in the Database

UBIQUITIN

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)