4YJF
Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003884 | molecular_function | D-amino-acid oxidase activity |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005737 | cellular_component | cytoplasm |
| 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 | 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 | 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 | 0005576 | cellular_component | extracellular region |
| B | 0005737 | cellular_component | cytoplasm |
| 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 | 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 | 0070945 | biological_process | neutrophil-mediated killing of gram-negative bacterium |
| B | 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 | GLY7 |
| A | THR44 |
| A | THR45 |
| A | ALA48 |
| A | ALA49 |
| A | GLY50 |
| A | LEU51 |
| A | ARG162 |
| A | VAL164 |
| A | CYS181 |
| A | THR182 |
| A | ALA8 |
| A | GLY183 |
| A | TRP185 |
| A | ILE202 |
| A | GLY281 |
| A | GLY312 |
| A | GLY313 |
| A | TYR314 |
| A | GLY315 |
| A | LEU316 |
| A | THR317 |
| A | GLY9 |
| A | 98B404 |
| A | HOH505 |
| A | HOH506 |
| A | HOH517 |
| A | HOH522 |
| A | VAL10 |
| A | ILE11 |
| A | ALA36 |
| A | ASP37 |
| A | ARG38 |
| A | THR43 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 402 |
| Chain | Residue |
| A | ARG286 |
| A | GLN288 |
| A | VAL289 |
| A | GLU292 |
| A | HOH525 |
| B | ARG22 |
| B | LYS328 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 403 |
| Chain | Residue |
| A | THR118 |
| A | PRO119 |
| A | ARG120 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue 98B A 404 |
| Chain | Residue |
| A | ALA49 |
| A | TYR224 |
| A | ILE230 |
| A | GLY313 |
| A | FAD401 |
| site_id | AC5 |
| Number of Residues | 33 |
| Details | binding site for residue FAD B 401 |
| Chain | Residue |
| 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 | ALA49 |
| B | GLY50 |
| B | LEU51 |
| B | ARG162 |
| B | VAL164 |
| B | CYS181 |
| B | THR182 |
| B | GLY183 |
| B | TRP185 |
| B | GLY281 |
| B | GLY312 |
| B | GLY313 |
| B | TYR314 |
| B | GLY315 |
| B | LEU316 |
| B | THR317 |
| B | 98B404 |
| B | HOH507 |
| B | HOH508 |
| B | HOH519 |
| B | HOH523 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 402 |
| Chain | Residue |
| B | HIS24 |
| B | ARG155 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 403 |
| Chain | Residue |
| A | ARG38 |
| A | LYS163 |
| B | ARG142 |
| B | GLN146 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue 98B B 404 |
| Chain | Residue |
| B | TYR224 |
| B | ILE230 |
| B | GLY313 |
| B | FAD401 |
Functional Information from PROSITE/UniProt
| site_id | PS00677 |
| Number of Residues | 19 |
| Details | DAO D-amino acid oxidases signature. VIHNYGhGGyGltihwGcA |
| Chain | Residue | Details |
| A | VAL305-ALA323 | |
| B | VAL305-ALA323 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:30333894, ECO:0000269|PubMed:8755502, ECO:0000269|PubMed:9153426, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1DDO, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:1VE9, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH, ECO:0007744|PDB:5WWV, ECO:0007744|PDB:5WX2 |
| Chain | Residue | Details |
| B | GLY312 | |
| B | GLY315 | |
| B | THR317 | |
| B | ALA8 | |
| B | ASP37 | |
| B | THR45 | |
| B | LEU51 | |
| B | VAL164 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 5 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P14920 |
| Chain | Residue | Details |
| B | GLY283 | |
| B | GLY9 | |
| B | THR43 | |
| B | GLN53 | |
| B | THR182 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27648606, ECO:0007744|PDB:4YJH |
| Chain | Residue | Details |
| B | VAL10 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:30333894, ECO:0000269|PubMed:8755502, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH, ECO:0007744|PDB:5WX2 |
| Chain | Residue | Details |
| B | ILE11 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:30333894, ECO:0000269|PubMed:9153426, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1DDO, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:1VE9, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH, ECO:0007744|PDB:5WWV, ECO:0007744|PDB:5WX2 |
| Chain | Residue | Details |
| B | ARG38 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:30333894, ECO:0000269|PubMed:8755502, ECO:0000269|PubMed:9153426, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1DDO, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:1VE9, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:5WWV |
| Chain | Residue | Details |
| B | THR44 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:8755502, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:1VE9, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH |
| Chain | Residue | Details |
| B | ALA49 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:30333894, ECO:0000269|PubMed:8755502, ECO:0000269|PubMed:9153426, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1DDO, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:1VE9, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH, ECO:0007744|PDB:5WWV |
| Chain | Residue | Details |
| B | GLY50 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0007744|PDB:1EVI |
| Chain | Residue | Details |
| B | LYS163 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:9399588, ECO:0007744|PDB:1AN9 |
| Chain | Residue | Details |
| B | TYR224 | |
| B | LEU228 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:9153426, ECO:0007744|PDB:1DDO, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH |
| Chain | Residue | Details |
| B | GLY313 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10876160, ECO:0000269|PubMed:24644036, ECO:0000269|PubMed:27648606, ECO:0000269|PubMed:30333894, ECO:0000269|PubMed:8755502, ECO:0000269|PubMed:9153426, ECO:0000269|PubMed:9399588, ECO:0007744|PDB:1AN9, ECO:0007744|PDB:1DDO, ECO:0007744|PDB:1EVI, ECO:0007744|PDB:1KIF, ECO:0007744|PDB:1VE9, ECO:0007744|PDB:3WGT, ECO:0007744|PDB:4YJD, ECO:0007744|PDB:4YJF, ECO:0007744|PDB:4YJG, ECO:0007744|PDB:4YJH, ECO:0007744|PDB:5WX2 |
| Chain | Residue | Details |
| B | LEU316 |
