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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P61864 New Search
12PDB entries
13Biological assembly
13chain/assembly records
Main Difference Dimensions in This Set
Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1OTR Solution Structure of a CUE-Ubiquitin Complex Deposited 2003-03-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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
1WR1 The complex structure of Dsk2p UBA with ubiquitin Deposited 2004-10-08 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule 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
1ZGU Solution structure of the human Mms2-Ubiquitin complex Deposited 2005-04-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.