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2len

Solution structure of UCHL1 S18Y variant

Method: SOLUTION NMR Dmax: 59.5 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

UniProt P09936

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：S18Y No other associated polymer 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

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 2LEN 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 method 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 method 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 method 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 method 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
3IFW Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester. Deposited 2009-07-26 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 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 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：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 method 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 method 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 method 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 experimental method 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 experimental method 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 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 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 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：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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–223（223 aa）
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
7ZM0 Structure of UCHL1 in complex with GK13S inhibitor Deposited 2022-04-18 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 1–223（223 aa）
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
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 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：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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 42 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 1–223； 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

SAXS profile for 2len

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2len
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2len
Deposition date deposition_date2011-06-19
Structure title titleSolution structure of UCHL1 S18Y variant
Keywords keywordshydrolase; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.43 Å
Radius of gyration Rg (electron density) rg_electron17.71 Å
Forward intensity I(0) i03867550000.00
Molecular weight molecular_weight519130.0 kDa
Excluded volume excluded_volume645200 ų
Envelope volume envelope_volume70022 ų
Hydration-shell volume shell_volume26921 ų
Envelope diameter envelope_diameter68.3 Å
Shell Rg shell_rg28.82 Å
Envelope Rg envelope_rg21.14 Å
Shape Rg shape_rg17.71 Å
Total Rg total_rg17.86 Å
Total atoms total_atoms65840
Residues n_residues4620
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax59.5 Å
Rg (real space) rg_real18.29 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real3.8680e+09
I(0) uncertainty (real space) i0_real_error5.0530e+07
Rg (reciprocal space) rg_reciprocal18.31 Å
I(0) (reciprocal space) i0_reciprocal3868000000.0000
Solution quality estimate total_estimate0.7942
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.4 Å
Skewness Skewness skewness0.077
Kurtosis Kurtosis kurtosis-0.387
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2890000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2lena1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.6 — Ubiquitin carboxyl-terminal hydrolase UCH-L
Domain ID domain_idd2lena2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2lenA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase
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8. Citations (1)

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9. Files and Curves (10)