4DM9
The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004197 | molecular_function | cysteine-type endopeptidase activity |
| A | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005789 | cellular_component | endoplasmic reticulum membrane |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006508 | biological_process | proteolysis |
| A | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| A | 0008233 | molecular_function | peptidase activity |
| A | 0008234 | molecular_function | cysteine-type peptidase activity |
| A | 0008242 | molecular_function | omega peptidase activity |
| A | 0016241 | biological_process | regulation of macroautophagy |
| A | 0016579 | biological_process | protein deubiquitination |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0030163 | biological_process | protein catabolic process |
| A | 0030424 | cellular_component | axon |
| A | 0030547 | molecular_function | signaling receptor inhibitor activity |
| A | 0031625 | molecular_function | ubiquitin protein ligase binding |
| A | 0031694 | molecular_function | alpha-2A adrenergic receptor binding |
| A | 0043022 | molecular_function | ribosome binding |
| A | 0043025 | cellular_component | neuronal cell body |
| A | 0043130 | molecular_function | ubiquitin binding |
| A | 0043161 | biological_process | proteasome-mediated ubiquitin-dependent protein catabolic process |
| A | 0043409 | biological_process | negative regulation of MAPK cascade |
| A | 0044306 | cellular_component | neuron projection terminus |
| A | 0045821 | biological_process | positive regulation of glycolytic process |
| A | 0071466 | biological_process | cellular response to xenobiotic stimulus |
| B | 0004197 | molecular_function | cysteine-type endopeptidase activity |
| B | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005789 | cellular_component | endoplasmic reticulum membrane |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006508 | biological_process | proteolysis |
| B | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| B | 0008233 | molecular_function | peptidase activity |
| B | 0008234 | molecular_function | cysteine-type peptidase activity |
| B | 0008242 | molecular_function | omega peptidase activity |
| B | 0016241 | biological_process | regulation of macroautophagy |
| B | 0016579 | biological_process | protein deubiquitination |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0030163 | biological_process | protein catabolic process |
| B | 0030424 | cellular_component | axon |
| B | 0030547 | molecular_function | signaling receptor inhibitor activity |
| B | 0031625 | molecular_function | ubiquitin protein ligase binding |
| B | 0031694 | molecular_function | alpha-2A adrenergic receptor binding |
| B | 0043022 | molecular_function | ribosome binding |
| B | 0043025 | cellular_component | neuronal cell body |
| B | 0043130 | molecular_function | ubiquitin binding |
| B | 0043161 | biological_process | proteasome-mediated ubiquitin-dependent protein catabolic process |
| B | 0043409 | biological_process | negative regulation of MAPK cascade |
| B | 0044306 | cellular_component | neuron projection terminus |
| B | 0045821 | biological_process | positive regulation of glycolytic process |
| B | 0071466 | biological_process | cellular response to xenobiotic stimulus |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR CHAIN X OF TRIPEPTIDE FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK |
| Chain | Residue |
| A | MET6 |
| A | CYS90 |
| A | ARG153 |
| A | ASN159 |
| A | PHE160 |
| A | ARG178 |
| A | PHE214 |
| A | SER215 |
| A | ALA216 |
| X | HOH101 |
| A | VAL31 |
| A | LEU32 |
| A | GLY33 |
| A | LEU34 |
| A | GLN84 |
| A | GLY87 |
| A | ASN88 |
| A | SER89 |
| site_id | AC2 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR CHAIN Y OF TRIPEPTIDE FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK |
| Chain | Residue |
| B | VAL31 |
| B | LEU32 |
| B | GLY33 |
| B | LEU34 |
| B | GLN84 |
| B | GLY87 |
| B | ASN88 |
| B | SER89 |
| B | CYS90 |
| B | ARG153 |
| B | LYS157 |
| B | VAL158 |
| B | ASN159 |
| B | PHE160 |
| B | ARG178 |
| B | PHE214 |
| Y | HOH101 |
Functional Information from PROSITE/UniProt
| site_id | PS00140 |
| Number of Residues | 17 |
| Details | UCH_1 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. QtigNSCGtigLIHAVA |
| Chain | Residue | Details |
| A | GLN84-ALA100 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Propeptide: {"description":"Removed in mature form","featureId":"PRO_0000414311","evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 438 |
| Details | Domain: {"description":"UCH catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 20 |
| Details | Region: {"description":"Interaction with ubiquitin","evidences":[{"source":"PubMed","id":"20439756","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20439756","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20439756","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 12 |
| Details | Site: {"description":"Susceptible to oxidation","evidences":[{"source":"PubMed","id":"14722078","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Site: {"description":"Transition state stabilizer","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"8639624","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Site: {"description":"Important for enzyme activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"37316325","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q00981","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Lipidation: {"description":"S-farnesyl cysteine","evidences":[{"source":"PubMed","id":"19261853","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
