SAXSdb — 1wr1

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

Ubiquitin

Saccharomyces cerevisiae

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 1–76	Not recorded	Ubiquitin-like protein DSK2 × 1 （P48510）	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 5mM potassium chloride NMR sample composition：U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O NMR sample composition：U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O	Resolution not provided

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 1WR1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OTR Solution Structure of a CUE-Ubiquitin Complex Deposited 2003-03-22	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 7.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 99.996% D2O NMR sample composition 1 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 99.996% D2O	Resolution not provided
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex Deposited 2003-07-17	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 100% D2O	Resolution not provided
1ZGU Solution structure of the human Mms2-Ubiquitin complex Deposited 2005-04-22	Different mutation/modification Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Mutation：K48R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR sample composition [U-15N; U-10% 13C]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20 NMR sample composition [U-13C; U-15N]-Ubiquitin + hMms2 (4:1 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20 NMR sample composition [U-13C; U-15N]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20	Resolution not provided
1ZW7 Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences Deposited 2005-06-03	Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：R42E, E34P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 30 mM actate；Pressure Ambient NMR sample composition 1-2 mM of appropriately labeled mutant ubiquitin \| 30 mM acetate buffer, pH 5.0	Resolution not provided
2G3Q Solution Structure of Ede1 UBA-ubiquitin complex Deposited 2006-02-20	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure 1 NMR sample composition 1mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O \| 100% D2O NMR sample composition 1mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O \| 100% D2O	Resolution not provided
2JT4 Solution Structure of the Sla1 SH3-3-Ubiquitin Complex Deposited 2007-07-18	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：SH3 domain sequence database residues 350-420	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 100% D2O \| 100% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 100% D2O \| 100% D2O	Resolution not provided
2JWZ Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins Deposited 2007-10-31	Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：L69S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20 mM；Pressure AMBIENT NMR sample composition 2 mM [U-100% 15N] L69S UBIQUITIN, 2 mM L69S UBIQUITIN, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2L00 Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin Deposited 2010-06-29	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：ubiquitin core domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 4 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 1 mM [U-100% 15N] ubiquitin-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-7, 50 uM Zinc-8, 4 mM MTSL-9, 5 mM TRIS-10, 50 mM sodium chloride-11, 4 mM ubiquitin-12, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-13, 50 uM Zinc-14, 0.1 mM DSS-15, 5 mM TRIS-16, 50 mM sodium chloride-17, 2 mM ubiquitin-18, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-19, 50 uM Zinc-20, 0.1 mM DSS-21, 5 mM TRIS-22, 50 mM sodium chloride-23, 5 % Polyacrylamide gel-24, 4 mM ubiquitin-25, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 4 mM ZNF216-A20-26, 50 uM Zinc-27, 0.1 mM DSS-28, 5 mM TRIS-29, 50 mM sodium chloride-30, 5 % Polyacrylamide gel-31, 1 mM [U-100% 15N] ubiquitin-32, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM ZNF216-A20-33, 50 uM Zinc-34, 0.1 mM DSS-35, 5 mM TRIS-36, 50 mM sodium chloride-37, 1 mM [U-100% 13C; U-100% 15N] ubiquitin-38, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] ZNF216-A20-39, 50 uM Zinc-40, 0.1 mM DSS-41, 5 mM TRIS-42, 50 mM sodium chloride-43, 4 mM ubiquitin-44, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23	Different ligand/ion Different experimental method 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	PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.247
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23	Different ligand/ion Different experimental method 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	PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.247
3L0W Structure of split monoubiquitinated PCNA with ubiquitin in position two Deposited 2009-12-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：ubi-C fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04 M ammonium sulfate, 0.1 M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.314
3L10 Structure of split monoubiquitinated PCNA with ubiquitin in position one Deposited 2009-12-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：Ubi-C fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04M ammonium sulfate, 0.1M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.314

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76

Ubiquitin-like protein DSK2

Saccharomyces cerevisiae

UniProt P48510

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 328–373	Fragment：C-TERMINAL UBA DOMAIN	Ubiquitin × 1 （P61864）	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 5mM potassium chloride NMR sample composition：U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O NMR sample composition：U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O	Resolution not provided

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 1WR1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	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 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain B 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain C 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain D 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain E 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain F 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain G 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain H 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain I 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain T 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain N 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain O 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain P 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain Q 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain R 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain U 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain J 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain K 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain L 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain M 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain S 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWF Crystal structure of the UBL domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct 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 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 1.15 Å R-free 0.195
2BWF Crystal structure of the UBL domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 1.15 Å R-free 0.195
3M63 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 Deposited 2010-03-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa） Fragment：UNP residues 1-75, Ubiquitin-like domain	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.270
4UN2 Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin Deposited 2014-05-23	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 328-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000	Resolution 1.51 Å R-free 0.196

5 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DSK2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 13–58； UniProt 328–373

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	1wr1
Deposition date deposition_date	2004-10-08
Structure title title	The complex structure of Dsk2p UBA with ubiquitin
Keywords keywords	UBA DOMAIN, UBA-UBIQUITIN COMPLEX, DSK2, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.60 Å
Radius of gyration Rg (electron density) rg_electron	16.24 Å
Forward intensity I(0) i0	1287650000.00
Molecular weight molecular_weight	294670.0 kDa
Excluded volume excluded_volume	365500 Å³
Envelope volume envelope_volume	42596 Å³
Hydration-shell volume shell_volume	17808 Å³
Envelope diameter envelope_diameter	74.9 Å
Shell Rg shell_rg	27.07 Å
Envelope Rg envelope_rg	23.43 Å
Shape Rg shape_rg	16.22 Å
Total Rg total_rg	16.47 Å
Total atoms total_atoms	41438
Residues n_residues	2679
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	67.5 Å
Rg (real space) rg_real	16.74 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.2880e+09
I(0) uncertainty (real space) i0_real_error	1.5990e+07
Rg (reciprocal space) rg_reciprocal	16.72 Å
I(0) (reciprocal space) i0_reciprocal	1288000000.0000
Solution quality estimate total_estimate	0.7358
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.5 Å
Skewness Skewness skewness	0.624
Kurtosis Kurtosis kurtosis	0.408
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	681200.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.358; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8568.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	41439

MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin-like protein DSK2
Molecular weight formula_weight	6181.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PGISGGGGGILDPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNGDV

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1wr1a_
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	d1wr1b1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d1wr1b2
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

CATH v4.4 (2 domains)

Domain ID domain_id	1wr1A00
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	1wr1B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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8. Citations (1)

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fit	/app/data/saxs_computation/wr/1wr1/1wr1.fit
pddf	/app/data/pr_computation/wr/1wr1/1wr1.pr.out
profile	/app/data/saxs_computation/wr/1wr1/1wr1.dat

The complex structure of Dsk2p UBA with ubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein DSK2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)