6KBP
Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003884 | molecular_function | D-amino-acid oxidase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005741 | cellular_component | mitochondrial outer membrane |
| A | 0005777 | cellular_component | peroxisome |
| A | 0005782 | cellular_component | peroxisomal matrix |
| A | 0005829 | cellular_component | cytosol |
| A | 0006562 | biological_process | proline catabolic process |
| A | 0007586 | biological_process | digestion |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0019478 | biological_process | D-amino acid catabolic process |
| A | 0036088 | biological_process | D-serine catabolic process |
| A | 0042416 | biological_process | dopamine biosynthetic process |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042995 | cellular_component | cell projection |
| A | 0045202 | cellular_component | synapse |
| A | 0046416 | biological_process | D-amino acid metabolic process |
| A | 0048786 | cellular_component | presynaptic active zone |
| A | 0055130 | biological_process | D-alanine catabolic process |
| A | 0070178 | biological_process | D-serine metabolic process |
| A | 0070945 | biological_process | neutrophil-mediated killing of gram-negative bacterium |
| A | 0071949 | molecular_function | FAD binding |
| B | 0003884 | molecular_function | D-amino-acid oxidase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005741 | cellular_component | mitochondrial outer membrane |
| B | 0005777 | cellular_component | peroxisome |
| B | 0005782 | cellular_component | peroxisomal matrix |
| B | 0005829 | cellular_component | cytosol |
| B | 0006562 | biological_process | proline catabolic process |
| B | 0007586 | biological_process | digestion |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0019478 | biological_process | D-amino acid catabolic process |
| B | 0036088 | biological_process | D-serine catabolic process |
| B | 0042416 | biological_process | dopamine biosynthetic process |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042995 | cellular_component | cell projection |
| B | 0045202 | cellular_component | synapse |
| B | 0046416 | biological_process | D-amino acid metabolic process |
| B | 0048786 | cellular_component | presynaptic active zone |
| B | 0055130 | biological_process | D-alanine catabolic process |
| B | 0070178 | biological_process | D-serine metabolic process |
| B | 0070945 | biological_process | neutrophil-mediated killing of gram-negative bacterium |
| B | 0071949 | molecular_function | FAD binding |
| C | 0003884 | molecular_function | D-amino-acid oxidase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005576 | cellular_component | extracellular region |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005741 | cellular_component | mitochondrial outer membrane |
| C | 0005777 | cellular_component | peroxisome |
| C | 0005782 | cellular_component | peroxisomal matrix |
| C | 0005829 | cellular_component | cytosol |
| C | 0006562 | biological_process | proline catabolic process |
| C | 0007586 | biological_process | digestion |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0019478 | biological_process | D-amino acid catabolic process |
| C | 0036088 | biological_process | D-serine catabolic process |
| C | 0042416 | biological_process | dopamine biosynthetic process |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0042995 | cellular_component | cell projection |
| C | 0045202 | cellular_component | synapse |
| C | 0046416 | biological_process | D-amino acid metabolic process |
| C | 0048786 | cellular_component | presynaptic active zone |
| C | 0055130 | biological_process | D-alanine catabolic process |
| C | 0070178 | biological_process | D-serine metabolic process |
| C | 0070945 | biological_process | neutrophil-mediated killing of gram-negative bacterium |
| C | 0071949 | molecular_function | FAD binding |
| D | 0003884 | molecular_function | D-amino-acid oxidase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005576 | cellular_component | extracellular region |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005741 | cellular_component | mitochondrial outer membrane |
| D | 0005777 | cellular_component | peroxisome |
| D | 0005782 | cellular_component | peroxisomal matrix |
| D | 0005829 | cellular_component | cytosol |
| D | 0006562 | biological_process | proline catabolic process |
| D | 0007586 | biological_process | digestion |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0019478 | biological_process | D-amino acid catabolic process |
| D | 0036088 | biological_process | D-serine catabolic process |
| D | 0042416 | biological_process | dopamine biosynthetic process |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0042995 | cellular_component | cell projection |
| D | 0045202 | cellular_component | synapse |
| D | 0046416 | biological_process | D-amino acid metabolic process |
| D | 0048786 | cellular_component | presynaptic active zone |
| D | 0055130 | biological_process | D-alanine catabolic process |
| D | 0070178 | biological_process | D-serine metabolic process |
| D | 0070945 | biological_process | neutrophil-mediated killing of gram-negative bacterium |
| D | 0071949 | molecular_function | FAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 34 |
| Details | binding site for residue FAD A 401 |
| Chain | Residue |
| A | ILE6 |
| A | THR43 |
| A | THR44 |
| A | THR45 |
| A | ALA48 |
| A | GLY50 |
| A | LEU51 |
| A | ARG162 |
| A | LYS163 |
| A | VAL164 |
| A | CYS181 |
| A | GLY7 |
| A | THR182 |
| A | GLY183 |
| A | TRP185 |
| A | ARG283 |
| A | GLY312 |
| A | GLY313 |
| A | TYR314 |
| A | GLY315 |
| A | LEU316 |
| A | THR317 |
| A | ALA8 |
| A | BEZ402 |
| A | HOH531 |
| A | HOH545 |
| A | HOH550 |
| A | HOH573 |
| A | GLY9 |
| A | VAL10 |
| A | ILE11 |
| A | ALA36 |
| A | ASP37 |
| A | ARG38 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue BEZ A 402 |
| Chain | Residue |
| A | TYR224 |
| A | TYR228 |
| A | ARG283 |
| A | GLY313 |
| A | FAD401 |
| site_id | AC3 |
| Number of Residues | 36 |
| Details | binding site for residue FAD B 401 |
| Chain | Residue |
| B | ILE6 |
| B | GLY7 |
| B | ALA8 |
| B | GLY9 |
| B | VAL10 |
| B | ILE11 |
| B | ALA36 |
| B | ASP37 |
| B | ARG38 |
| B | THR43 |
| B | THR44 |
| B | THR45 |
| B | ALA48 |
| B | GLY50 |
| B | LEU51 |
| B | ARG162 |
| B | VAL164 |
| B | CYS181 |
| B | THR182 |
| B | GLY183 |
| B | TRP185 |
| B | HIS311 |
| B | GLY312 |
| B | GLY313 |
| B | TYR314 |
| B | GLY315 |
| B | LEU316 |
| B | THR317 |
| B | BEZ402 |
| B | ACT403 |
| B | HOH512 |
| B | HOH516 |
| B | HOH520 |
| B | HOH522 |
| B | HOH534 |
| B | HOH542 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue BEZ B 402 |
| Chain | Residue |
| B | TYR224 |
| B | TYR228 |
| B | ILE230 |
| B | ARG283 |
| B | GLY313 |
| B | FAD401 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue ACT B 403 |
| Chain | Residue |
| B | ASP37 |
| B | FAD401 |
| site_id | AC6 |
| Number of Residues | 34 |
| Details | binding site for residue FAD C 401 |
| Chain | Residue |
| C | VAL164 |
| C | CYS181 |
| C | THR182 |
| C | GLY183 |
| C | TRP185 |
| C | ARG283 |
| C | HIS311 |
| C | GLY312 |
| C | GLY313 |
| C | TYR314 |
| C | GLY315 |
| C | LEU316 |
| C | THR317 |
| C | BEZ402 |
| C | HOH506 |
| C | HOH522 |
| C | HOH539 |
| C | HOH571 |
| C | GLY7 |
| C | ALA8 |
| C | GLY9 |
| C | VAL10 |
| C | ILE11 |
| C | ALA36 |
| C | ASP37 |
| C | ARG38 |
| C | THR43 |
| C | THR44 |
| C | THR45 |
| C | ALA48 |
| C | GLY50 |
| C | LEU51 |
| C | ARG162 |
| C | LYS163 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue BEZ C 402 |
| Chain | Residue |
| C | TYR224 |
| C | TYR228 |
| C | ARG283 |
| C | GLY313 |
| C | FAD401 |
| site_id | AC8 |
| Number of Residues | 36 |
| Details | binding site for residue FAD D 401 |
| Chain | Residue |
| D | ILE6 |
| D | GLY7 |
| D | ALA8 |
| D | GLY9 |
| D | VAL10 |
| D | ILE11 |
| D | ALA36 |
| D | ASP37 |
| D | ARG38 |
| D | THR43 |
| D | THR44 |
| D | THR45 |
| D | ALA48 |
| D | GLY50 |
| D | LEU51 |
| D | ARG162 |
| D | VAL164 |
| D | CYS181 |
| D | THR182 |
| D | GLY183 |
| D | TRP185 |
| D | ARG283 |
| D | HIS311 |
| D | GLY312 |
| D | GLY313 |
| D | TYR314 |
| D | GLY315 |
| D | LEU316 |
| D | THR317 |
| D | BEZ402 |
| D | ACT403 |
| D | HOH526 |
| D | HOH533 |
| D | HOH535 |
| D | HOH545 |
| D | HOH587 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue BEZ D 402 |
| Chain | Residue |
| D | TYR224 |
| D | TYR228 |
| D | ARG283 |
| D | GLY313 |
| D | FAD401 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue ACT D 403 |
| Chain | Residue |
| D | ASP37 |
| D | FAD401 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
| Chain | Residue | Details |
| A | ALA8 | |
| A | ILE11 | |
| B | ALA8 | |
| B | ILE11 | |
| C | ALA8 | |
| C | ILE11 | |
| D | ALA8 | |
| D | ILE11 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17303072, ECO:0007744|PDB:2E4A, ECO:0007744|PDB:2E82 |
| Chain | Residue | Details |
| A | GLY9 | |
| B | GLY9 | |
| C | GLY9 | |
| D | GLY9 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17088322, ECO:0000269|PubMed:23566269, ECO:0000269|PubMed:23631755, ECO:0007744|PDB:2DU8, ECO:0007744|PDB:3W4I, ECO:0007744|PDB:3W4J, ECO:0007744|PDB:3W4K, ECO:0007744|PDB:3ZNO, ECO:0007744|PDB:3ZNQ |
| Chain | Residue | Details |
| A | VAL10 | |
| B | VAL10 | |
| C | VAL10 | |
| D | VAL10 |
| Chain | Residue | Details |
| A | ASP37 | |
| B | ASP37 | |
| C | ASP37 | |
| D | ASP37 |
| Chain | Residue | Details |
| A | ARG38 | |
| B | VAL164 | |
| B | GLY312 | |
| B | THR317 | |
| C | ARG38 | |
| C | THR45 | |
| C | LEU51 | |
| C | VAL164 | |
| C | GLY312 | |
| C | THR317 | |
| D | ARG38 | |
| A | THR45 | |
| D | THR45 | |
| D | LEU51 | |
| D | VAL164 | |
| D | GLY312 | |
| D | THR317 | |
| A | LEU51 | |
| A | VAL164 | |
| A | GLY312 | |
| A | THR317 | |
| B | ARG38 | |
| B | THR45 | |
| B | LEU51 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18455394, ECO:0007744|PDB:3CUK |
| Chain | Residue | Details |
| A | THR43 | |
| B | THR43 | |
| C | THR43 | |
| D | THR43 |
| Chain | Residue | Details |
| A | THR44 | |
| B | THR44 | |
| C | THR44 | |
| D | THR44 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P00371 |
| Chain | Residue | Details |
| A | ALA49 | |
| A | LYS163 | |
| B | ALA49 | |
| B | LYS163 | |
| C | ALA49 | |
| C | LYS163 | |
| D | ALA49 | |
| D | LYS163 |
| Chain | Residue | Details |
| A | GLY50 | |
| B | GLY50 | |
| C | GLY50 | |
| D | GLY50 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17303072, ECO:0007744|PDB:2E82 |
| Chain | Residue | Details |
| A | GLN53 | |
| B | GLN53 | |
| C | GLN53 | |
| D | GLN53 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0007744|PDB:3ZNQ |
| Chain | Residue | Details |
| A | THR182 | |
| B | THR182 | |
| C | THR182 | |
| D | THR182 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:17303072, ECO:0007744|PDB:2E4A |
| Chain | Residue | Details |
| A | TYR224 | |
| B | TYR224 | |
| C | TYR224 | |
| D | TYR224 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:17088322, ECO:0000305|PubMed:17303072, ECO:0000305|PubMed:18455394, ECO:0007744|PDB:2DU8, ECO:0007744|PDB:2E4A, ECO:0007744|PDB:3CUK |
| Chain | Residue | Details |
| A | TYR228 | |
| B | TYR228 | |
| C | TYR228 | |
| D | TYR228 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17303072, ECO:0000269|PubMed:18455394, ECO:0000269|PubMed:23566269, ECO:0000269|PubMed:23631755, ECO:0007744|PDB:2E48, ECO:0007744|PDB:2E49, ECO:0007744|PDB:2E82, ECO:0007744|PDB:3CUK, ECO:0007744|PDB:3W4I, ECO:0007744|PDB:3W4J, ECO:0007744|PDB:3W4K, ECO:0007744|PDB:3ZNO |
| Chain | Residue | Details |
| A | ARG283 | |
| B | ARG283 | |
| C | ARG283 | |
| D | ARG283 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17088322, ECO:0000269|PubMed:17303072, ECO:0000269|PubMed:23566269, ECO:0000269|PubMed:23631755, ECO:0000269|PubMed:25001371, ECO:0007744|PDB:2DU8, ECO:0007744|PDB:2E48, ECO:0007744|PDB:2E49, ECO:0007744|PDB:2E82, ECO:0007744|PDB:3W4I, ECO:0007744|PDB:3W4J, ECO:0007744|PDB:3W4K, ECO:0007744|PDB:3ZNO, ECO:0007744|PDB:3ZNP, ECO:0007744|PDB:3ZNQ, ECO:0007744|PDB:4QFD |
| Chain | Residue | Details |
| A | GLY313 | |
| B | GLY313 | |
| C | GLY313 | |
| D | GLY313 |
| Chain | Residue | Details |
| A | GLY315 | |
| B | GLY315 | |
| C | GLY315 | |
| D | GLY315 |
| Chain | Residue | Details |
| A | LEU316 | |
| B | LEU316 | |
| C | LEU316 | |
| D | LEU316 |
