5f6y

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)

Method: X-RAY DIFFRACTION D_max: 57.1 Å Quality: GOOD

▼

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

SUMO-conjugating enzyme UBC9

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–158	Mutation：K48A,K49A,E54A	5VM 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000	Resolution 1.14 Å R-free 0.178

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 5F6Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3S HUMAN UBC9 Deposited 1998-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.	Resolution 2.80 Å R-free 0.260
1KPS Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1 Deposited 2002-01-02	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 A 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.0M ammonium phosphate, 0.1M hepes, 10mM CuCl2, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.300
1KPS Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1 Deposited 2002-01-02	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 C 1–158（158 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.0M ammonium phosphate, 0.1M hepes, 10mM CuCl2, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.300
1Z5S Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2 Deposited 2005-03-19	Different construct 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 A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG4000 (w/v), 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.01 Å R-free 0.290
2GRN Crystal Structure of human RanGAP1-Ubc9 Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.218
2GRO Crystal Structure of human RanGAP1-Ubc9-N85Q Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa）	Mutation：N85Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.202
2GRP Crystal Structure of human RanGAP1-Ubc9-Y87A Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa）	Mutation：Y87A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.05 Å R-free 0.231
2GRQ Crystal Structure of human RanGAP1-Ubc9-D127A Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa）	Mutation：D127A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.205
2GRR Crystal Structure of human RanGAP1-Ubc9-D127S Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa）	Mutation：D127S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.30 Å R-free 0.222
2O25 Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9 Deposited 2006-11-29	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 D 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.60 Å R-free 0.291
2O25 Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9 Deposited 2006-11-29	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 C 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.60 Å R-free 0.291
2PE6 Non-covalent complex between human SUMO-1 and human Ubc9 Deposited 2007-04-02	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 A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；291 K；100 mM Tris-HCl, pH 8.5, 25% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50	Resolution 2.40 Å R-free 0.250
2PX9 The intrinsic affinity between E2 and the Cys domain of E1 in Ubiquitin-like modifications Deposited 2007-05-14	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 × 2 PDB declaration: dimeric	Chain B 1–158（158 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM Phosphate；Pressure 1 NMR sample composition 0.15-0.6mM E1 Cys domain, 0.15-0.7mM Ubc9, 50mM Phosphate buffer \| 50mM Phosphate buffer	Resolution not provided
2XWU CRYSTAL STRUCTURE OF IMPORTIN 13 - UBC9 COMPLEX Deposited 2010-11-05	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 A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；50 MM MES PH 6.5 25% PEG 300	Resolution 2.80 Å R-free 0.268
3A4S The crystal structure of the SLD2:Ubc9 complex Deposited 2009-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.269
3A4S The crystal structure of the SLD2:Ubc9 complex Deposited 2009-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.269
3UIN Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 Deposited 2011-11-05	Different construct 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 A 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.60 Å R-free 0.264
3UIO Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct 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 A 1–158（158 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；pH 6；279 K；14% PEG4000, 100 mM sodium citrate pH 6.0, 200 mM ammonium acetate, vapor diffusion, hanging drop, temperature 279K	Resolution 2.60 Å R-free 0.251
3UIP Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct 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 A 1–158（158 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；pH 7.5；279 K；22% PEG4000, 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.29 Å R-free 0.232
4W5V Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd) Deposited 2014-08-19	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 A 1–158（158 aa）	Not recorded	FMT FORMIC ACID × 1 GOL GLYCEROL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；100 mM Tris, pH 8.0, 20% PEG MME 550, 200 mM potassium formate, 20% glycerol; seeded	Resolution 2.50 Å R-free 0.283
4Y1L Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation Deposited 2015-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–158（158 aa） Chain B 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；10% (w/v) PEG8000, 100 mM HEPES, pH 8.0, 8% ethylene glycol	Resolution 2.70 Å R-free 0.278
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05	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 A 1–158（158 aa）	Mutation：K14R	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5	Resolution 2.40 Å R-free 0.234
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05	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 1–158（158 aa）	Mutation：K14R	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5	Resolution 2.40 Å R-free 0.234
5F6D Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6 Deposited 2015-12-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：K48A,K49A,E54A	5VJ 6~{H}-benzo[c][1,2]benzothiazine 5,5-dioxide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000	Resolution 1.55 Å R-free 0.196
5F6E Crystal Structure of human Ubc9 (K48A/K49A/E54A) Deposited 2015-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：K48A,K49A,E54A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol	Resolution 1.12 Å R-free 0.170
5F6U Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146) Deposited 2015-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：K48A,K49A,K54A	5VK ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol	Resolution 1.55 Å R-free 0.203
5F6V Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from fragment cocktail screen) Deposited 2015-12-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：K48A,K49A,E54A	5VL 2-(2-hydroxyphenyl)phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000	Resolution 1.49 Å R-free 0.184
5F6W Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol) Deposited 2015-12-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：K48A,K49A,E54A	5VL 2-(2-hydroxyphenyl)phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol	Resolution 1.70 Å R-free 0.200
5F6X Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen) Deposited 2015-12-07	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–158（157 aa）	Mutation：K48A,K49A,E54A	5VM 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000	Resolution 1.56 Å R-free 0.193
5FQ2 Crystal structure of human SUMO E1 UFD domain in complex with Ubc9 in a P422 space group. Deposited 2015-12-04	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 A 1–158（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.249
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–158（157 aa）	Mutation：K48A, K49A, E54A, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000	Resolution 1.90 Å R-free 0.263
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–158（157 aa）	Mutation：K48A, K49A, E54A, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000	Resolution 1.90 Å R-free 0.263
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–158（157 aa）	Mutation：K48A, K49A, E54A, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000	Resolution 1.90 Å R-free 0.263
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 2–158（157 aa）	Mutation：K48A, K49A, E54A, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000	Resolution 1.90 Å R-free 0.263
8ODR Mimetic of UBC9-SUMO1 Deposited 2023-03-09	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 2–158（157 aa）	Mutation：K14R, A129K	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；LiSO4, Tris pH8.5, PEG 4000	Resolution 2.85 Å R-free 0.258
9B62 Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model Deposited 2024-03-23	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 × 7 PDB declaration: heptameric	Chain C 1–158（158 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 2.90 Å
9DQB Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex. Deposited 2024-09-23	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 × 5 PDB declaration: pentameric	Chain C 1–158（158 aa）	Mutation：F22A,G23Q,V25S,A129K,C138S,K153R	AMP ADENOSINE MONOPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9DRJ Cryo-EM structure of a SUMO E1-E2-SUMO1 complex. Deposited 2024-09-25	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 × 4 PDB declaration: tetrameric	Chain C 1–158（158 aa）	Mutation：C138S	ZN ZINC ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9GLR Crystal Structure of Human UBC9 C93E Deposited 2024-08-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–158（158 aa）	Mutation：C93E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；2% tacsimate, pH 5.0, 0.1 M sodium citrate, 16% PEG 3350	Resolution 1.72 Å R-free 0.227

32 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBC9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 2–158

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5f6y
Deposition date deposition_date	2015-12-07
Structure title title	Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
Keywords keywords	Ubc9, Fragment drug design, sumoylation, LIGASE-LIGASE inhibitor complex; LIGASE/LIGASE inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.20 Å
Radius of gyration Rg (electron density) rg_electron	16.02 Å
Forward intensity I(0) i0	5795830.00
Molecular weight molecular_weight	17788.0 kDa
Excluded volume excluded_volume	22399 Å³
Envelope volume envelope_volume	25408 Å³
Hydration-shell volume shell_volume	13763 Å³
Envelope diameter envelope_diameter	55.7 Å
Shell Rg shell_rg	21.52 Å
Envelope Rg envelope_rg	16.36 Å
Shape Rg shape_rg	15.99 Å
Total Rg total_rg	17.11 Å
Total atoms total_atoms	1252
Residues n_residues	156
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

▼

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

Maximum dimension Dmax dmax	57.1 Å
Rg (real space) rg_real	17.17 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	5.7960e+06
I(0) uncertainty (real space) i0_real_error	6.9370e+04
Rg (reciprocal space) rg_reciprocal	17.17 Å
I(0) (reciprocal space) i0_reciprocal	5796000.0000
Solution quality estimate total_estimate	0.8818
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.310
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	999200.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.949

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SUMO-conjugating enzyme UBC9
Molecular weight formula_weight	17725.4 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	K48A,K49A,E54A
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	1563

SGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

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 2 Entity 2 non-polymer

Description description	5-chloranyl-3~{H}-1,3-benzoxazole-2-thione
Molecular weight formula_weight	185.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5f6ya_
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.20.1.1 — UBC-related

CATH v4.4 (1 domains)

Domain ID domain_id	5f6yA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

▶

8. Citations (1)

▶

Unit-cell length a length_a	50.237 Å
Unit-cell length b length_b	35.492 Å
Unit-cell length c length_c	58.122 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.140 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1567
R_work r_work	0.1556
R_free r_free	0.1778

fit	/app/data/saxs_computation/f6/5f6y/5f6y.fit
pddf	/app/data/pr_computation/f6/5f6y/5f6y.pr.out
profile	/app/data/saxs_computation/f6/5f6y/5f6y.dat