4ip3

Complex structure of OspI and Ubc13

Method: X-RAY DIFFRACTION D_max: 72.8 Å Quality: GOOD

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

ORF169b

Shigella flexneri

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 1–212	Mutation：C62A	Ubiquitin-conjugating enzyme E2 N × 1 （P61088）	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

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 4IP3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3B21 Crystal structure of OspI from Shigella flexineri Deposited 2011-07-19	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–212（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.1M MES, 0.1M NaAcetate, 1.0M NaCl, 24%(w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.01 Å R-free 0.226
3W30 Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI Deposited 2012-12-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–212（212 aa）	Mutation：C62A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Magnesium Acetate, 0.1M Tris-HCl (pH6.5), 25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.99 Å R-free 0.303
3W30 Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI Deposited 2012-12-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–212（212 aa）	Mutation：C62A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Magnesium Acetate, 0.1M Tris-HCl (pH6.5), 25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.99 Å R-free 0.303
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 A 1–212（212 aa）	Mutation：C62A	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
4XZX Shigella flexneri effector OspI C62S mutant Deposited 2015-02-05	Different mutation/modification 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 1–212（212 aa）	Mutation：C62S	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.2M magnesium acetate, 0.1M sodium cacodylate, 20% PEG8000	Resolution 2.20 Å R-free 0.246

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

View Construct and Data Evidence

UniProt name	Q8VSD5_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–214； UniProt 1–212

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	ORF169b × 1 （Q8VSD5）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4IP3	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
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
9BIV Crystal Structure of Ubc13 with a New Active Site Loop Conformation Deposited 2024-04-24	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 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
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 21–172； 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	4ip3
Deposition date deposition_date	2013-01-09
Structure title title	Complex structure of OspI and Ubc13
Keywords keywords	Papain fold, UNKNOWN FUNCTION-Ligase complex; UNKNOWN FUNCTION/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	22.79 Å
Radius of gyration Rg (electron density) rg_electron	21.75 Å
Forward intensity I(0) i0	25529300.00
Molecular weight molecular_weight	38224.0 kDa
Excluded volume excluded_volume	47690 Å³
Envelope volume envelope_volume	57022 Å³
Hydration-shell volume shell_volume	22229 Å³
Envelope diameter envelope_diameter	75.1 Å
Shell Rg shell_rg	28.42 Å
Envelope Rg envelope_rg	21.99 Å
Shape Rg shape_rg	21.74 Å
Total Rg total_rg	22.62 Å
Total atoms total_atoms	2689
Residues n_residues	343
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	72.8 Å
Rg (real space) rg_real	22.79 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.5530e+07
I(0) uncertainty (real space) i0_real_error	2.9050e+05
Rg (reciprocal space) rg_reciprocal	22.79 Å
I(0) (reciprocal space) i0_reciprocal	25530000.0000
Solution quality estimate total_estimate	0.8999
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.408
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5628000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.991

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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	ORF169b
Molecular weight formula_weight	23478.1 kDa
Mutation mutation	C62A
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	2837

GSMINGVSLQGTAGYEAHTEEGNVNVKKLLESLNSKSLGDMDKDSELAATLQKMINPSGGDGNASGCALHACMAMLGYGVREAPVPNEISEYMTGFFHRHLEQIDSEGIVSHPNETYSKFRERIAENILQNTSKGSVVMISIEQATHWIAGFNDGEKIMFLDVQTGKGFNLYDPVEKSPDAFVDENSSVQVIHVSDQEFDHYANSSSWKSKRLC

来源 Source

来源生物 organism	Shigella flexneri
NCBI Class编号 ncbi_taxonomy_id	623
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 N
Molecular weight formula_weight	19329.2 kDa
EC 编号 ec_number	6.3.2.19
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ip3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4ip3A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	4ip3B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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8. Citations (1)

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Unit-cell length a length_a	119.060 Å
Unit-cell length b length_b	119.060 Å
Unit-cell length c length_c	69.735 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	34.020 Å
R factor r_factor	0.2140
R_work r_work	0.2100
R_free r_free	0.2480

fit	/app/data/saxs_computation/ip/4ip3/4ip3.fit
pddf	/app/data/pr_computation/ip/4ip3/4ip3.pr.out
profile	/app/data/saxs_computation/ip/4ip3/4ip3.dat

Complex structure of OspI and Ubc13

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

ORF169b

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

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)