4YIH
Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000255 | biological_process | allantoin metabolic process |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005829 | cellular_component | cytosol |
| A | 0006204 | biological_process | IMP catabolic process |
| A | 0006249 | biological_process | dCMP catabolic process |
| A | 0008252 | molecular_function | nucleotidase activity |
| A | 0008253 | molecular_function | 5'-nucleotidase activity |
| A | 0009117 | biological_process | nucleotide metabolic process |
| A | 0009223 | biological_process | pyrimidine deoxyribonucleotide catabolic process |
| A | 0009264 | biological_process | deoxyribonucleotide catabolic process |
| A | 0016311 | biological_process | dephosphorylation |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016791 | molecular_function | phosphatase activity |
| A | 0019103 | molecular_function | pyrimidine nucleotide binding |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0043605 | biological_process | amide catabolic process |
| A | 0046050 | biological_process | UMP catabolic process |
| A | 0046055 | biological_process | dGMP catabolic process |
| A | 0046074 | biological_process | dTMP catabolic process |
| A | 0046079 | biological_process | dUMP catabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050483 | molecular_function | IMP 5'-nucleotidase activity |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000255 | biological_process | allantoin metabolic process |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005829 | cellular_component | cytosol |
| B | 0006204 | biological_process | IMP catabolic process |
| B | 0006249 | biological_process | dCMP catabolic process |
| B | 0008252 | molecular_function | nucleotidase activity |
| B | 0008253 | molecular_function | 5'-nucleotidase activity |
| B | 0009117 | biological_process | nucleotide metabolic process |
| B | 0009223 | biological_process | pyrimidine deoxyribonucleotide catabolic process |
| B | 0009264 | biological_process | deoxyribonucleotide catabolic process |
| B | 0016311 | biological_process | dephosphorylation |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016791 | molecular_function | phosphatase activity |
| B | 0019103 | molecular_function | pyrimidine nucleotide binding |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0043605 | biological_process | amide catabolic process |
| B | 0046050 | biological_process | UMP catabolic process |
| B | 0046055 | biological_process | dGMP catabolic process |
| B | 0046074 | biological_process | dTMP catabolic process |
| B | 0046079 | biological_process | dUMP catabolic process |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050483 | molecular_function | IMP 5'-nucleotidase activity |
| B | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 201 |
| Chain | Residue |
| A | ASP10 |
| A | ASP12 |
| A | ASP145 |
| A | PO4202 |
| A | 2O2203 |
| A | GOL204 |
| A | HOH358 |
| site_id | AC2 |
| Number of Residues | 12 |
| Details | binding site for residue PO4 A 202 |
| Chain | Residue |
| A | ASP12 |
| A | THR99 |
| A | SER100 |
| A | LYS134 |
| A | MG201 |
| A | 2O2203 |
| A | HOH358 |
| A | HOH313 |
| A | HOH351 |
| A | HOH377 |
| A | ASP10 |
| A | MET11 |
| site_id | AC3 |
| Number of Residues | 17 |
| Details | binding site for residue 2O2 A 203 |
| Chain | Residue |
| A | ASP12 |
| A | PHE18 |
| A | PHE44 |
| A | LEU45 |
| A | ALA46 |
| A | ARG47 |
| A | TYR65 |
| A | SER100 |
| A | LEU102 |
| A | LEU103 |
| A | ARG132 |
| A | MG201 |
| A | PO4202 |
| A | GOL204 |
| A | HOH316 |
| A | HOH351 |
| A | HOH377 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | binding site for residue GOL A 204 |
| Chain | Residue |
| A | ASP12 |
| A | GLY13 |
| A | PHE18 |
| A | GLU19 |
| A | PHE44 |
| A | ASP145 |
| A | CYS165 |
| A | HIS167 |
| A | MG201 |
| A | 2O2203 |
| A | HOH310 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 201 |
| Chain | Residue |
| B | ASP10 |
| B | ASP12 |
| B | ASP145 |
| B | PO4202 |
| B | 2O2203 |
| B | HOH344 |
| site_id | AC6 |
| Number of Residues | 11 |
| Details | binding site for residue PO4 B 202 |
| Chain | Residue |
| B | ASP10 |
| B | MET11 |
| B | ASP12 |
| B | THR99 |
| B | SER100 |
| B | LYS112 |
| B | LYS134 |
| B | MG201 |
| B | 2O2203 |
| B | HOH344 |
| B | HOH317 |
| site_id | AC7 |
| Number of Residues | 15 |
| Details | binding site for residue 2O2 B 203 |
| Chain | Residue |
| B | ASP12 |
| B | PHE18 |
| B | PHE44 |
| B | LEU45 |
| B | ALA46 |
| B | ARG47 |
| B | TYR65 |
| B | LEU102 |
| B | LEU103 |
| B | ARG132 |
| B | MG201 |
| B | PO4202 |
| B | HOH344 |
| B | HOH314 |
| B | HOH304 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Nucleophile => ECO:0000305 |
| Chain | Residue | Details |
| A | ASP10 | |
| B | ASP10 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton donor => ECO:0000305 |
| Chain | Residue | Details |
| A | ASP12 | |
| B | ASP12 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 10 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ASP10 | |
| B | ASP145 | |
| A | ASP12 | |
| A | PHE18 | |
| A | PHE44 | |
| A | ASP145 | |
| B | ASP10 | |
| B | ASP12 | |
| B | PHE18 | |
| B | PHE44 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000250 |
| Chain | Residue | Details |
| A | TYR65 | |
| B | TYR65 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305 |
| Chain | Residue | Details |
| A | THR99 | |
| A | LYS134 | |
| B | THR99 | |
| B | LYS134 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER182 | |
| B | SER182 |
