7zm0

Structure of UCHL1 in complex with GK13S inhibitor

Method: X-RAY DIFFRACTION D_max: 111.3 Å Quality: GOOD

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

Ubiquitin carboxyl-terminal hydrolase isozyme L1

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 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 1–223	Mutation：lysine-dimethylated	JMF (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4	Resolution 2.24 Å R-free 0.288

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 7ZM0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ETL Crystal Structure of Ubiquitin Carboxy-terminal Hydrolase L1 (UCH-L1) Deposited 2005-10-27	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 1–223（223 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.4 M Ammonium Sulfate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.274
2ETL Crystal Structure of Ubiquitin Carboxy-terminal Hydrolase L1 (UCH-L1) Deposited 2005-10-27	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 1–223（223 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.4 M Ammonium Sulfate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.274
2ETL Crystal Structure of Ubiquitin Carboxy-terminal Hydrolase L1 (UCH-L1) Deposited 2005-10-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 1–223（223 aa）	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.4 M Ammonium Sulfate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.274
2ETL Crystal Structure of Ubiquitin Carboxy-terminal Hydrolase L1 (UCH-L1) Deposited 2005-10-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–223（223 aa）	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.4 M Ammonium Sulfate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.274
2LEN Solution structure of UCHL1 S18Y variant Deposited 2011-06-19	Different mutation/modification 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 1–223（223 aa）	Mutation：S18Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 0.7-0.8mM [U-99% 13C; U-99% 15N] UCHL1 S18Y variant-1, 20mM sodium phosphate-2, 100mM sodium chloride-3, 3mM DTT-4, 90% H2O-5, 10% D2O-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3IFW Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester. Deposited 2009-07-26	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 A 1–223（223 aa）	Mutation：S18Y	GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；2.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.256
3IRT Crystal Structure of the I93M Mutant of Ubiquitin Carboxy-terminal Hydrolase L1 Deposited 2009-08-24	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 1–223（223 aa）	Mutation：I93M	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4 M Ammonium Sulfate, 0.1 M TRIS Hydrochloride, 0.1 M Sodium Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.254
3IRT Crystal Structure of the I93M Mutant of Ubiquitin Carboxy-terminal Hydrolase L1 Deposited 2009-08-24	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 1–223（223 aa）	Mutation：I93M	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4 M Ammonium Sulfate, 0.1 M TRIS Hydrochloride, 0.1 M Sodium Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.254
3KVF Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30	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 1–223（223 aa）	Mutation：I93M	GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.284
3KW5 Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester Deposited 2009-11-30	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 1–223（223 aa）	Not recorded	GVE METHYL 4-AMINOBUTANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.83 Å R-free 0.286
4DM9 The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK Deposited 2012-02-07	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 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4M ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.35 Å R-free 0.250
4DM9 The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK Deposited 2012-02-07	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 B 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4M ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.35 Å R-free 0.250
4JKJ Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1 Deposited 2013-03-09	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 1–223（223 aa）	Mutation：S18Y	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4M Ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.15 Å R-free 0.245
4JKJ Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1 Deposited 2013-03-09	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 1–223（223 aa）	Mutation：S18Y	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4M Ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.15 Å R-free 0.245
4JKJ Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1 Deposited 2013-03-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–223（223 aa）	Mutation：S18Y	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4M Ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.15 Å R-free 0.245
4JKJ Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1 Deposited 2013-03-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 1–223（223 aa）	Mutation：S18Y	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4M Ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.15 Å R-free 0.245
8DY8 Crystal structure of the R178Q mutant of ubiquitin carboxy terminal hydrolase L1 (UCH-L1) Deposited 2022-08-03	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 1–223（223 aa）	Mutation：R178Q	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；2.4 M Ammonium Sulfate, 0.1 M HEPES	Resolution 2.10 Å R-free 0.265
8DY8 Crystal structure of the R178Q mutant of ubiquitin carboxy terminal hydrolase L1 (UCH-L1) Deposited 2022-08-03	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 1–223（223 aa）	Mutation：R178Q	SO4 SULFATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；2.4 M Ammonium Sulfate, 0.1 M HEPES	Resolution 2.10 Å R-free 0.265
8EDE Crystal structure of covalent inhibitor 2-chloro-N'-(N-(4-chlorophenyl)-N-methylglycyl)acetohydrazide bound to Ubiquitin C-terminal Hydrolase-L1 Deposited 2022-09-04	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 1–223（223 aa）	Not recorded	WEU 2-[(4-chlorophenyl)-methyl-amino]-~{N}'-ethanoyl-ethanehydrazide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294.15 K；0.1M tri-Sodium citrate 2.4M Ammonium sulfate	Resolution 1.80 Å R-free 0.227
8EDE Crystal structure of covalent inhibitor 2-chloro-N'-(N-(4-chlorophenyl)-N-methylglycyl)acetohydrazide bound to Ubiquitin C-terminal Hydrolase-L1 Deposited 2022-09-04	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 1–223（223 aa）	Not recorded	WEU 2-[(4-chlorophenyl)-methyl-amino]-~{N}'-ethanoyl-ethanehydrazide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294.15 K；0.1M tri-Sodium citrate 2.4M Ammonium sulfate	Resolution 1.80 Å R-free 0.227
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	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 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	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 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8PW1 Structure of human UCHL1 in complex with CG341 inhibitor Deposited 2023-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 1–223（223 aa）	Not recorded	GKO (2~{S})-4-(iminomethyl)-1-methyl-~{N}-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]piperazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.49 M ammonium sulfate, 85 mM trisodium citrate	Resolution 2.20 Å R-free 0.271
8XI7 The Crystal Structure of UCHL1 from Biortus. Deposited 2023-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–223（223 aa） Chain B 1–223（223 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.1M ammonium sulfate, 2% PEG 400, 100mM HEPES, pH 7.0	Resolution 1.95 Å R-free 0.231
9O4M Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine Deposited 2025-04-08	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 1–223（223 aa）	Mutation：Q209C	6NA HEXANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid	Resolution 2.00 Å R-free 0.262
9O4M Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine Deposited 2025-04-08	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 A 1–223（223 aa）	Mutation：Q209C	6NA HEXANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid	Resolution 2.00 Å R-free 0.262

13 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UCHL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–227； UniProt 1–223 Author chain B； PDBConstruct 5–227； UniProt 1–223 Author chain C； PDBConstruct 5–227； UniProt 1–223 Author chain D； PDBConstruct 5–227； UniProt 1–223 Author chain E； PDBConstruct 5–227； UniProt 1–223 Author chain F； PDBConstruct 5–227； UniProt 1–223 Author chain G； PDBConstruct 5–227； UniProt 1–223 Author chain H； PDBConstruct 5–227； UniProt 1–223 Author chain I； PDBConstruct 5–227； UniProt 1–223 Author chain J； PDBConstruct 5–227； UniProt 1–223

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	7zm0
Deposition date deposition_date	2022-04-18
Structure title title	Structure of UCHL1 in complex with GK13S inhibitor
Keywords keywords	DUB, UCHL1, UCH-L1, UCHL-1, deubiquitinase, ubiquitin, cyanopyrrolidine, inhibitor, HYDROLASE; HYDROLASE
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	39.43 Å
Radius of gyration Rg (electron density) rg_electron	38.23 Å
Forward intensity I(0) i0	770415000.00
Molecular weight molecular_weight	225410.0 kDa
Excluded volume excluded_volume	281080 Å³
Envelope volume envelope_volume	380980 Å³
Hydration-shell volume shell_volume	78344 Å³
Envelope diameter envelope_diameter	115.1 Å
Shell Rg shell_rg	48.18 Å
Envelope Rg envelope_rg	36.87 Å
Shape Rg shape_rg	38.25 Å
Total Rg total_rg	38.71 Å
Total atoms total_atoms	15864
Residues n_residues	2117
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	111.3 Å
Rg (real space) rg_real	38.96 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	7.7040e+08
I(0) uncertainty (real space) i0_real_error	1.0890e+07
Rg (reciprocal space) rg_reciprocal	39.26 Å
I(0) (reciprocal space) i0_reciprocal	770600000.0000
Solution quality estimate total_estimate	0.8279
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	55.6 Å
Skewness Skewness skewness	-0.111
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	243000000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase isozyme L1
Molecular weight formula_weight	25153.6 kDa
EC 编号 ec_number	3.4.19.12
Mutation mutation	lysine-dimethylated
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	16195

GPGSMQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA

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	(3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide
Molecular weight formula_weight	392.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	331

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8. Citations (1)

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Unit-cell length a length_a	101.926 Å
Unit-cell length b length_b	144.414 Å
Unit-cell length c length_c	158.250 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	40

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

Resolution resolution	2.240 Å
Low-resolution limit resolution_low	62.500 Å
R factor r_factor	0.2413
R_work r_work	0.2401
R_free r_free	0.2878

fit	/app/data/saxs_computation/zm/7zm0/7zm0.fit
pddf	/app/data/pr_computation/zm/7zm0/7zm0.pr.out
profile	/app/data/saxs_computation/zm/7zm0/7zm0.dat