9biv

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

Method: X-RAY DIFFRACTION D_max: 75.8 Å Quality: GOOD

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

Ubiquitin-conjugating enzyme E2 variant 2

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 1–145	Not recorded	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7.5；298 K；Ubc13-Mms2 heterodimer was concentrated to 12 mg/mL and stored in 50 mM Tris pH 7.5, 150 mM NaCl, 1mM TCEP. Complex was left to slowly equilibrate from 277K to 298 overnight	Resolution 1.68 Å R-free 0.177

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 9BIV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J74 Crystal Structure of Mms2 Deposited 2001-05-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–145（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；16% PEG 6000, 25mM NaCl, 100mM citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.246
1J7D Crystal Structure of hMms2-hUbc13 Deposited 2001-05-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–145（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 8000, 100mM Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.244
1ZGU Solution structure of the human Mms2-Ubiquitin complex Deposited 2005-04-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 7–145（139 aa）	Not recorded	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
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain W 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain a 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain d 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain f 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain h 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain k 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 17 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain m 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 18 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain o 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 6–143（138 aa） Fragment：UNP residues 6-143	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
4NR3 Crystal Structure of a human Mms2/Ubc13 L121G mutant Deposited 2013-11-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 6–145（140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K	Resolution 1.80 Å R-free 0.234
4NRG Crystal Structure of a human Mms2/Ubc13 D118G mutant Deposited 2013-11-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–145（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K	Resolution 1.95 Å R-free 0.211
4NRI Crystal Structure of a human Mms2/Ubc13 A122G mutant Deposited 2013-11-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 6–145（140 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K	Resolution 2.30 Å R-free 0.235
4ONL Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P Deposited 2014-01-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–145（145 aa）	Mutation：R85S, A122V, N123P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.35 Å R-free 0.199
4ONM Crystal structure of human Mms2/Ubc13 - NSC697923 Deposited 2014-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–145（145 aa）	Not recorded	GOL GLYCEROL × 1 N2F 2-[(4-methylphenyl)sulfonyl]-5-nitrofuran × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.35 Å R-free 0.192
4ONN Crystal structure of human Mms2/Ubc13 - BAY 11-7082 Deposited 2014-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–145（145 aa）	Not recorded	GOL GLYCEROL × 3 BY1 3-[(4-methylphenyl)sulfonyl]prop-2-enenitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.213
4ORH Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer Deposited 2014-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–145（145 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.80 Å R-free 0.282
4ORH Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer Deposited 2014-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–145（145 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.80 Å R-free 0.282
4ORH Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer Deposited 2014-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–145（145 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.80 Å R-free 0.282
5AIT A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–145（145 aa） Fragment：UNP RESIDUES 1-145 Chain G 1–145（145 aa） Fragment：UNP RESIDUES 1-145	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.286
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–145（145 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K	Resolution 2.20 Å R-free 0.252
7BBF Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2 Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 1–145（145 aa） Chain E 1–145（145 aa） Chain H 1–145（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M bicine Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2 % of each Anesthetic alkaloids (lidocaine HCl H2O, procaine HCl, proparacaine HCl, tetracaine HCl)	Resolution 2.54 Å R-free 0.253
8WR5 The Crystal Structure of Mms2 from Biortus Deposited 2023-10-13	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 1–145（145 aa）	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li2SO4,0.1 M NaAC pH5.5,10% PEG 1000,10% PEG 8000	Resolution 1.70 Å R-free 0.210
8WR5 The Crystal Structure of Mms2 from Biortus Deposited 2023-10-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–145（145 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li2SO4,0.1 M NaAC pH5.5,10% PEG 1000,10% PEG 8000	Resolution 1.70 Å R-free 0.210
9LHJ UBE2N/UBE2V2 complexed with a covalent inhibitor Deposited 2025-01-12	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–145（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M BIS-TRIS pH 6.5, 20% w/v PEG 5,000	Resolution 1.68 Å R-free 0.228
9LHJ UBE2N/UBE2V2 complexed with a covalent inhibitor Deposited 2025-01-12	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–145（145 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M BIS-TRIS pH 6.5, 20% w/v PEG 5,000	Resolution 1.68 Å R-free 0.228
9N1F Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex Deposited 2025-01-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–145（145 aa）	Mutation：S32A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium Malonate and 18% w/v PEG 3350	Resolution 2.10 Å R-free 0.279

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

View Construct and Data Evidence

UniProt name	UB2V2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–145； UniProt 1–145

Ubiquitin-conjugating enzyme E2 N

Homo sapiens

UniProt P61088

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 1–152	Not recorded	Ubiquitin-conjugating enzyme E2 variant 2 × 1 （Q15819）	X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7.5；298 K；Ubc13-Mms2 heterodimer was concentrated to 12 mg/mL and stored in 50 mM Tris pH 7.5, 150 mM NaCl, 1mM TCEP. Complex was left to slowly equilibrate from 277K to 298 overnight	Resolution 1.68 Å R-free 0.177

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9BIV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J7D Crystal Structure of hMms2-hUbc13 Deposited 2001-05-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 8000, 100mM Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.244
2C2V Crystal structure of the CHIP-UBC13-UEV1a complex Deposited 2005-09-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 2–152（151 aa） Chain H 2–152（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；MCHIP(166-304), UBC13 AND UEV1A WERE COMBINED IN A 1:1:1 MOLAR RATIO, INCUBATED FOR 30 MIN, AND CONCENTRATED TO 10 MG/ML BY ULTRAFILTRATION. CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C AGAINST 20% (W/V) PEG2000 MME, 100 MM TRIS-HCL (PH 7.0).	Resolution 2.90 Å R-free 0.297
2C2V Crystal structure of the CHIP-UBC13-UEV1a complex Deposited 2005-09-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 2–152（151 aa） Chain K 2–152（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；MCHIP(166-304), UBC13 AND UEV1A WERE COMBINED IN A 1:1:1 MOLAR RATIO, INCUBATED FOR 30 MIN, AND CONCENTRATED TO 10 MG/ML BY ULTRAFILTRATION. CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C AGAINST 20% (W/V) PEG2000 MME, 100 MM TRIS-HCL (PH 7.0).	Resolution 2.90 Å R-free 0.297
3HCT Crystal structure of TRAF6 in complex with Ubc13 in the P1 space group Deposited 2009-05-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；8% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.278
3HCU Crystal structure of TRAF6 in complex with Ubc13 in the C2 space group Deposited 2009-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa） Fragment：Ubc13	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；16-20% PEG 4000, 0.2M Magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.333
3HCU Crystal structure of TRAF6 in complex with Ubc13 in the C2 space group Deposited 2009-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–152（152 aa） Fragment：Ubc13	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；16-20% PEG 4000, 0.2M Magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.333
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain b 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain e 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain g 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain i 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain l 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 17 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain n 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 18 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain p 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3VON Crystalstructure of the ubiquitin protease Deposited 2012-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 3–150（148 aa） Fragment：UNP residues 3-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；90mM Tris-HCl buffer (pH 8.5), 19% PEG 3350, 10mM EDTA sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.281
3W31 Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI Deposited 2012-12-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.4M potassium iodide, 0.1M MES (pH6.5), 4mM DTT, 15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.96 Å R-free 0.284
4DHI Structure of C. elegans OTUB1 bound to human UBC13 Deposited 2012-01-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–152（152 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；100 mM sodium cacodylate, 1 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.209
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–152（152 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；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–152（152 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；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–152（152 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；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 1–152（152 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；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.237
4DHZ The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub Deposited 2012-01-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–152（152 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；21% PEG10000, 0.1 M sodium chloride, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.11 Å R-free 0.288
4IP3 Complex structure of OspI and Ubc13 Deposited 2013-01-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；0.2 M Sodium thiocyanate, 20% PEG3350, 0.1 M HEPES pH7.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.30 Å R-free 0.248
4NR3 Crystal Structure of a human Mms2/Ubc13 L121G mutant Deposited 2013-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–150（149 aa）	Mutation：L121G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K	Resolution 1.80 Å R-free 0.234
4NRG Crystal Structure of a human Mms2/Ubc13 D118G mutant Deposited 2013-11-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Mutation：D118G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K	Resolution 1.95 Å R-free 0.211
4NRI Crystal Structure of a human Mms2/Ubc13 A122G mutant Deposited 2013-11-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–150（148 aa）	Mutation：A122G	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K	Resolution 2.30 Å R-free 0.235
4ONL Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P Deposited 2014-01-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.35 Å R-free 0.199
4ONM Crystal structure of human Mms2/Ubc13 - NSC697923 Deposited 2014-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	GOL GLYCEROL × 1 N2F 2-[(4-methylphenyl)sulfonyl]-5-nitrofuran × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.35 Å R-free 0.192
4ONN Crystal structure of human Mms2/Ubc13 - BAY 11-7082 Deposited 2014-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	GOL GLYCEROL × 3 BY1 3-[(4-methylphenyl)sulfonyl]prop-2-enenitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.213
4ORH Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer Deposited 2014-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 1–152（152 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.80 Å R-free 0.282
4ORH Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer Deposited 2014-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–152（152 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.80 Å R-free 0.282
4ORH Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer Deposited 2014-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–152（152 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.80 Å R-free 0.282
4TKP Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor Deposited 2014-05-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M bis-tris	Resolution 2.08 Å R-free 0.255
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–152（152 aa） Fragment：unp residues 1-152 Chain E 1–152（152 aa） Fragment：unp residues 1-152	Mutation：C87K Mutation：C87K	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4	Resolution 8.30 Å R-free 0.337
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 1–152（152 aa） Fragment：unp residues 1-152 Chain K 1–152（152 aa） Fragment：unp residues 1-152	Mutation：C87K Mutation：C87K	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4	Resolution 8.30 Å R-free 0.337
5AIT A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–152（152 aa） Chain E 1–152（152 aa）	Mutation：YES Mutation：YES	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.286
5AIU A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–152（152 aa） Chain E 1–152（152 aa）	Mutation：YES Mutation：YES	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions 1,2-ETHANEDIOL	Resolution 2.21 Å R-free 0.255
5EYA TRIM25 RING domain in complex with Ubc13-Ub conjugate Deposited 2015-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa）	Mutation：C87K Mutation：C87K	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li citrate, 20% PEG 3350	Resolution 2.40 Å R-free 0.228
5H7S Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain Deposited 2016-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–152（152 aa） Chain C 1–152（152 aa）	Mutation：C87K, K92A Mutation：C87K, K92A	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350	Resolution 3.49 Å R-free 0.286
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–152（152 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350	Resolution 3.41 Å R-free 0.294
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–152（152 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350	Resolution 3.41 Å R-free 0.294
5VO0 Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–152（152 aa） Chain E 1–152（152 aa）	Not recorded	ZN ZINC ION × 8 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5	Resolution 3.90 Å R-free 0.299
5YWR Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13) Deposited 2017-11-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 1 FMT FORMIC ACID × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2M Magnesium fromate dihydrate, 20% PEG 3350 (w/v)	Resolution 1.47 Å R-free 0.184
6D6I Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13 Deposited 2018-04-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 3–152（150 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2M LiSO4, 25% PEG3350, 0.1 M Tris-HCl pH 8.5	Resolution 2.55 Å R-free 0.296
6D6I Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13 Deposited 2018-04-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 3–152（150 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2M LiSO4, 25% PEG3350, 0.1 M Tris-HCl pH 8.5	Resolution 2.55 Å R-free 0.296
6JKY Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila Deposited 2019-03-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–152（152 aa）	Mutation：K94A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350	Resolution 2.45 Å R-free 0.258
6JKY Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila Deposited 2019-03-03	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 1–152（152 aa）	Mutation：K94A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350	Resolution 2.45 Å R-free 0.258
6KFP Crystal structure of MavC ternary complex Deposited 2019-07-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, lithium chloride	Resolution 2.92 Å R-free 0.250
6KG6 Crystal structure of MavC/UBE2N-Ub complex Deposited 2019-07-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 4000, Tris	Resolution 2.39 Å R-free 0.245
6KL4 Crystal structure of MavC-UBE2N-Ub Deposited 2019-07-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–152（152 aa）	Mutation：K94A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；289.15 K；0.2M Sodium malonate pH 6.0, 20%w/v PEG 3,350	Resolution 2.85 Å R-free 0.262
6LP2 Structure of Lpg2148/UBE2N-Ub complex Deposited 2020-01-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, potassium citrate	Resolution 2.48 Å R-free 0.233
6P5B Crystal Structure of MavC in Complex with Ub-UbE2N Deposited 2019-05-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.2 M Na Malonate, 25% PEG 3350, 10 mM NiCl2	Resolution 2.10 Å R-free 0.232
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–152（152 aa） Chain E 1–152（152 aa）	Not recorded	ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.	Resolution 2.80 Å R-free 0.249
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 1–152（152 aa） Chain K 1–152（152 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.	Resolution 2.80 Å R-free 0.249
6ULH Structure of MavC in complex with its substrate in R3 spacegroup Deposited 2019-10-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；0.1 M Sodium Acetate: HCl, pH 4.6 3.5 M Sodium Formate	Resolution 1.97 Å R-free 0.227
6UMP Crystal structure of MavC in complex with substrate mimic in P65 space group Deposited 2019-10-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium formate, 20% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.304
6UMS Crystal structure of MavC in complex with its substrate mimic in C222(1) space group Deposited 2019-10-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.15 M Potassium bromide, 30% (w/v) PEG 2000 MME	Resolution 2.34 Å R-free 0.250
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–152（152 aa）	Mutation：C87K, K92A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K	Resolution 2.20 Å R-free 0.252
7BBF Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2 Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–152（152 aa） Chain D 1–152（152 aa） Chain G 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M bicine Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2 % of each Anesthetic alkaloids (lidocaine HCl H2O, procaine HCl, proparacaine HCl, tetracaine HCl)	Resolution 2.54 Å R-free 0.253
7BXG MavC-UBE2N-Ub complex Deposited 2020-04-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M sodium malonate, pH 7.0, 12% PEG3350	Resolution 2.71 Å R-free 0.243
9LHJ UBE2N/UBE2V2 complexed with a covalent inhibitor Deposited 2025-01-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa）	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；289.15 K；0.1 M BIS-TRIS pH 6.5, 20% w/v PEG 5,000	Resolution 1.68 Å R-free 0.228
9LHJ UBE2N/UBE2V2 complexed with a covalent inhibitor Deposited 2025-01-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	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；289.15 K；0.1 M BIS-TRIS pH 6.5, 20% w/v PEG 5,000	Resolution 1.68 Å R-free 0.228
9N1F Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex Deposited 2025-01-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–152（152 aa）	Mutation：C87K, K92T, K94Q	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium Malonate and 18% w/v PEG 3350	Resolution 2.10 Å R-free 0.279
9UV6 Encounter complex structure of E2N and Ubiquitin Deposited 2025-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–152（150 aa）	Mutation：N123C	A1EQF (5~{S},16~{S})-16-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylamino]-2,11,12,17-tetraoxa-5,8-diaza-1$l^{4}-manganatricyclo[6.3.3.3^{1,5}]heptadecane-3,10,13-trione × 1	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure 1 NMR sample composition 0.6 mM [U-15N] Ubi, 0.2 mM E2N, 20 mM HEPES, 90 % H2O, 10 % [U-2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

43 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBE2N_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–152； UniProt 1–152

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	9biv
Deposition date deposition_date	2024-04-24
最后修订 last_revision	2024-05-08
Structure title title	Crystal Structure of Ubc13 with a New Active Site Loop Conformation
Keywords keywords	E2, Conjugating, Enzyme, Ubiquitin, Ubc13, Mms2, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.51 Å
Radius of gyration Rg (electron density) rg_electron	22.55 Å
Forward intensity I(0) i0	18373800.00
Molecular weight molecular_weight	32605.0 kDa
Excluded volume excluded_volume	40968 Å³
Envelope volume envelope_volume	50147 Å³
Hydration-shell volume shell_volume	19614 Å³
Envelope diameter envelope_diameter	79.1 Å
Shell Rg shell_rg	28.06 Å
Envelope Rg envelope_rg	22.57 Å
Shape Rg shape_rg	22.51 Å
Total Rg total_rg	23.42 Å
Total atoms total_atoms	4599
Residues n_residues	288
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	75.8 Å
Rg (real space) rg_real	23.56 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.8370e+07
I(0) uncertainty (real space) i0_real_error	2.5550e+05
Rg (reciprocal space) rg_reciprocal	23.56 Å
I(0) (reciprocal space) i0_reciprocal	18370000.0000
Solution quality estimate total_estimate	0.8883
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3410000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.928

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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	Ubiquitin-conjugating enzyme E2 variant 2
Molecular weight formula_weight	16380.7 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	5041

MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 N
Molecular weight formula_weight	17157.8 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

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 BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	442

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8. Citations (1)

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Unit-cell length a length_a	86.361 Å
Unit-cell length b length_b	42.942 Å
Unit-cell length c length_c	93.790 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	42.684 Å
R factor r_factor	0.1454
R_work r_work	0.1438
R_free r_free	0.1766

fit	/app/data/saxs_computation/bi/9biv/9biv.fit
pddf	/app/data/pr_computation/bi/9biv/9biv.pr.out
profile	/app/data/saxs_computation/bi/9biv/9biv.dat

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

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

Ubiquitin-conjugating enzyme E2 variant 2

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2 N

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)