SAXSdb — 4q5h

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

Protein kinase OspG

Shigella sonnei

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 26–196	Fragment：unp residues 26-193	Polyubiquitin × 1 （P0CG63） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228

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 4Q5H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Q5E Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate Deposited 2014-04-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–196（171 aa） Fragment：unp residues 26-193	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.87 Å R-free 0.232

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

View Construct and Data Evidence

UniProt name	OSPG_SHISS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–174； UniProt 26–196

Polyubiquitin

Saccharomyces cerevisiae

UniProt P0CG63

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–76	Mutation：C17S, C137S	Protein kinase OspG × 1 （Q3YTH2） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228

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 4Q5H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3OLM Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT Ubiquitin Ligase Deposited 2010-08-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；13.5% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.272
4HCN Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin Deposited 2012-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：unp RESIDUES 1-76	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 FMT FORMIC ACID × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.2；293 K；12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K	Resolution 2.60 Å R-free 0.260
4NNJ Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin Deposited 2013-11-18	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 1–76（76 aa） Fragment：UNP residues 1-76 Chain D 1–76（76 aa） Fragment：UNP residues 1-76 Chain E 1–76（76 aa） Fragment：UNP residues 1-76	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 29 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15% (w/v) polyethylene glycol 3350, 100mM lithium sulfate and 100mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.201
4Q5E Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate Deposited 2014-04-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa）	Mutation：C17S, C137S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.87 Å R-free 0.232
8DAT Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB) Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.80 Å
8DAU Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.70 Å
8DAV Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uC) Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.50 Å
8DAW Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.60 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric	Chain H 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBI4P_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76

Ubiquitin-conjugating enzyme E2 L3

Homo sapiens

UniProt P68036

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–154	Mutation：K48R, G76C	Protein kinase OspG × 1 （Q3YTH2） Polyubiquitin × 1 （P0CG63） MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228

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 4Q5H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C4Z STRUCTURE OF AN E6AP-UBCH7 COMPLEX: INSIGHTS INTO THE UBIQUITINATION PATHWAY Deposited 1999-10-14	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 D 1–154（154 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG1500, MAGNESIUM CHLORIDE, MES-NA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.60 Å R-free 0.290
1FBV STRUCTURE OF A CBL-UBCH7 COMPLEX: RING DOMAIN FUNCTION IN UBIQUITIN-PROTEIN LIGASES Deposited 2000-07-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–154（154 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；Sodium Citrate, Ammonium Sulfate,, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
3SQV Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7 Deposited 2011-07-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–154（154 aa）	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.5-1.7 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.30 Å R-free 0.298
3SQV Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7 Deposited 2011-07-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–154（154 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.5-1.7 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.30 Å R-free 0.298
3SQV Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7 Deposited 2011-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–154（154 aa） Chain D 1–154（154 aa）	Not recorded	SO4 SULFATE ION × 9 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.5-1.7 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.30 Å R-free 0.298
3SY2 Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7 Deposited 2011-07-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–154（154 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.27 Å R-free 0.275
3SY2 Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7 Deposited 2011-07-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–154（154 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.27 Å R-free 0.275
4Q5E Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate Deposited 2014-04-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–154（154 aa）	Mutation：K48R, G76C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.87 Å R-free 0.232
5HPT System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7 Deposited 2016-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–154（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；isopropanol 10%, PEG3350 8%, sodium citrate 0.1 M	Resolution 2.84 Å R-free 0.237
5HPT System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7 Deposited 2016-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 2–154（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；isopropanol 10%, PEG3350 8%, sodium citrate 0.1 M	Resolution 2.84 Å R-free 0.237
5TTE Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester intermediate mimic Deposited 2016-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–154（154 aa） Fragment：unp residues 1-154	Mutation：C17S, C86K	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.17；291 K；0.1M Sodium Cacodylate pH6.17, 0.35M Sodium Acetate, 10% Glycerol	Resolution 3.50 Å R-free 0.252
5UDH HHARI/ARIH1-UBCH7~Ubiquitin Deposited 2016-12-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–154（154 aa） Fragment：UNP residues 1-154	Mutation：C86K	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；1 ul protein mixture with 10-12 mg/ml protein in 25 mM Tris pH 7.0, 150 mM NaCl, 1 mM DTT and 1 ul well solution with 7-10% PEG 5000 MME, 0.1 M HP pH 7.0 and 5% Tascimate pH 7.0. Over 1 ml reservoir.	Resolution 3.24 Å R-free 0.279
5UDH HHARI/ARIH1-UBCH7~Ubiquitin Deposited 2016-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–154（154 aa） Fragment：UNP residues 1-154	Mutation：C86K	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；1 ul protein mixture with 10-12 mg/ml protein in 25 mM Tris pH 7.0, 150 mM NaCl, 1 mM DTT and 1 ul well solution with 7-10% PEG 5000 MME, 0.1 M HP pH 7.0 and 5% Tascimate pH 7.0. Over 1 ml reservoir.	Resolution 3.24 Å R-free 0.279
6CP2 SidC in complex with UbcH7~Ub Deposited 2018-03-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–154（154 aa）	Mutation：C86K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；16% PEG 3000, 0.1 M Tris pH 9.0	Resolution 2.90 Å R-free 0.288
6DJW Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex Deposited 2018-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–154（154 aa）	Mutation：C86K	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1 M Tris-HCl, pH 8.0, 15% w/v PEG2000 MME, 0.1 M potasssium chloride	Resolution 3.80 Å R-free 0.297
6DJX Crystal Structure of pParkin-pUb-UbcH7 complex Deposited 2018-05-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–154（154 aa）	Mutation：C86K	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M HEPES, pH 6.5, 6% isopropanol, 50 mM magnesium chloride, 5% w/v PEG4000	Resolution 4.80 Å R-free 0.290
6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–154（154 aa）	Mutation：C17S, C86K, C137S	ZN ZINC ION × 8	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6XXU Solution NMR structure of the native form of UbcH7 (UBE2L3) Deposited 2020-01-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–154（154 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.9 mM [U-99% 15N] UbcH7 E2 Enzyme, 50 mM potassium phosphate, 0.25 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-99% 13C; U-99% 15N] UbcH7 E2 Enzyme, 50 mM potassium phosphate, 0.25 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 1–154（154 aa）	Mutation：C17A, C137A	ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–154（154 aa）	Not recorded	ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7OIK Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized Deposited 2021-05-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–154（154 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7V8F Crystal structure of UBE2L3 bound to HOIP RING1 domain. Deposited 2021-08-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–154（154 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；289 K；2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(w/v) PEG 3,350.	Resolution 1.66 Å R-free 0.198
8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30	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 1–154（154 aa）	Mutation：C86K	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2	Resolution 3.08 Å R-free 0.266
8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–154（154 aa）	Mutation：C86K	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2	Resolution 3.08 Å R-free 0.266
8EB0 RNF216/E2-Ub/Ub transthiolation complex Deposited 2022-08-30	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 1–154（154 aa）	Mutation：C86K	ZN ZINC ION × 7 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；2 M ammonium sulfate	Resolution 3.03 Å R-free 0.339
9I1J Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS Deposited 2025-01-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–154（154 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å

20 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UB2L3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–156； UniProt 1–154

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4q5h
Deposition date deposition_date	2014-04-16
Structure title title	Shigella Effector Kinase OspG bound to AMPPNP and E2-Ub UbcH7-Ub Conjugate
Keywords keywords	;protein-protein complex, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, kinase fold, inhibition of NF-kB pathway, UNKNOWN FUNCTION, PROTEIN BINDING ;; UNKNOWN FUNCTION, PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	25.28 Å
Radius of gyration Rg (electron density) rg_electron	24.37 Å
Forward intensity I(0) i0	36142200.00
Molecular weight molecular_weight	46228.0 kDa
Excluded volume excluded_volume	57831 Å³
Envelope volume envelope_volume	70651 Å³
Hydration-shell volume shell_volume	24581 Å³
Envelope diameter envelope_diameter	81.5 Å
Shell Rg shell_rg	30.85 Å
Envelope Rg envelope_rg	24.38 Å
Shape Rg shape_rg	24.36 Å
Total Rg total_rg	25.18 Å
Total atoms total_atoms	3253
Residues n_residues	400
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	78.4 Å
Rg (real space) rg_real	25.22 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.6140e+07
I(0) uncertainty (real space) i0_real_error	4.3700e+05
Rg (reciprocal space) rg_reciprocal	25.24 Å
I(0) (reciprocal space) i0_reciprocal	36140000.0000
Solution quality estimate total_estimate	0.9107
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.209
Kurtosis Kurtosis kurtosis	-0.615
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8826000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Protein kinase OspG
Molecular weight formula_weight	20116.5 kDa
EC 编号 ec_number	2.7.-.-
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	3546

SNAEPILGKLIGQGSTAEIFEDVNDSSALYKKYDLIGNQYNEILEMAWQESELFNAFYGDEASVVIQYGGDVYLRMLRVPGTPLSDIDTADIPDNIESLYLQLICKLNELSIIHYDLNTGNMLYDKESESLFPIDFRNIYAEYYAATKKDKEIIDRRLQMRTNDFYSLLNRKYL

来源 Source

来源生物 organism	Shigella sonnei
NCBI Class编号 ncbi_taxonomy_id	300269
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polyubiquitin
Molecular weight formula_weight	8642.9 kDa
EC 编号 ec_number	6.3.2.19
Mutation mutation	C17S, C137S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLRLRGC

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin-conjugating enzyme E2 L3
Molecular weight formula_weight	18052.7 kDa
EC 编号 ec_number	6.3.2.19
Mutation mutation	K48R, G76C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GHMAASRRLMKELEEIRKSGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFSKNAEEFTKKYGEKRPVD

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 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4q5hb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d4q5hc1
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

Domain ID domain_id	d4q5hc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	4q5hA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4q5hA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4q5hC00
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	67.416 Å
Unit-cell length b length_b	84.658 Å
Unit-cell length c length_c	85.873 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.999 Å
Low-resolution limit resolution_low	44.939 Å
R factor r_factor	0.1922
R_work r_work	0.1903
R_free r_free	0.2278

fit	/app/data/saxs_computation/q5/4q5h/4q5h.fit
pddf	/app/data/pr_computation/q5/4q5h/4q5h.pr.out
profile	/app/data/saxs_computation/q5/4q5h/4q5h.dat

Shigella Effector Kinase OspG bound to AMPPNP and E2-Ub UbcH7-Ub Conjugate

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

Protein kinase OspG

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2 L3

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)