4PAB
Crystal structure of the precursor form of rat DMGDH complexed with tetrahydrofolate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005542 | molecular_function | folic acid binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0006579 | biological_process | amino-acid betaine catabolic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0019695 | biological_process | choline metabolic process |
| A | 0035999 | biological_process | tetrahydrofolate interconversion |
| A | 0042426 | biological_process | choline catabolic process |
| A | 0047865 | molecular_function | dimethylglycine dehydrogenase activity |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0005542 | molecular_function | folic acid binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0006579 | biological_process | amino-acid betaine catabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0019695 | biological_process | choline metabolic process |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0042426 | biological_process | choline catabolic process |
| B | 0047865 | molecular_function | dimethylglycine dehydrogenase activity |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 17 |
| Details | binding site for residue THG A 902 |
| Chain | Residue |
| A | ILE560 |
| A | PHE717 |
| A | TYR737 |
| A | SCN906 |
| A | HOH1130 |
| A | HOH1181 |
| A | HOH1182 |
| A | HOH1282 |
| A | HOH1304 |
| A | GLU573 |
| A | THR575 |
| A | ILE587 |
| A | PHE649 |
| A | LEU650 |
| A | TYR669 |
| A | GLU676 |
| A | TYR678 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue SCN A 903 |
| Chain | Residue |
| A | TYR103 |
| A | THR152 |
| A | HOH1290 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue SCN A 904 |
| Chain | Residue |
| A | TYR571 |
| A | ARG598 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | binding site for residue SCN A 905 |
| Chain | Residue |
| A | ASP618 |
| A | ARG681 |
| site_id | AC5 |
| Number of Residues | 9 |
| Details | binding site for residue SCN A 906 |
| Chain | Residue |
| A | PHE649 |
| A | ILE667 |
| A | SER668 |
| A | GLY671 |
| A | THR843 |
| A | PRO845 |
| A | THG902 |
| A | HOH1130 |
| A | HOH1258 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | binding site for residue THG B 902 |
| Chain | Residue |
| B | ILE560 |
| B | GLU573 |
| B | THR575 |
| B | ILE587 |
| B | PHE649 |
| B | LEU650 |
| B | TYR669 |
| B | GLU676 |
| B | TYR678 |
| B | PHE717 |
| B | TYR737 |
| B | HOH1112 |
| B | HOH1303 |
| B | HOH1327 |
| B | HOH1329 |
| B | HOH1331 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue SCN B 903 |
| Chain | Residue |
| B | TYR103 |
| B | THR152 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue SCN B 904 |
| Chain | Residue |
| B | TYR571 |
| B | ARG598 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue SCN B 905 |
| Chain | Residue |
| B | TRP428 |
| B | ARG463 |
| B | ASP618 |
| B | HOH1113 |
| B | HOH1332 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue SCN B 906 |
| Chain | Residue |
| A | GLN851 |
| B | GLN851 |
| site_id | AD2 |
| Number of Residues | 40 |
| Details | binding site for residue FAD A 901 |
| Chain | Residue |
| A | HOH1308 |
| A | ILE48 |
| A | GLY49 |
| A | GLY50 |
| A | GLY51 |
| A | CYS52 |
| A | VAL53 |
| A | LEU72 |
| A | GLU73 |
| A | LYS74 |
| A | ALA79 |
| A | GLY80 |
| A | SER81 |
| A | THR82 |
| A | HIS84 |
| A | ALA85 |
| A | ALA86 |
| A | GLY87 |
| A | LEU88 |
| A | PRO211 |
| A | VAL212 |
| A | ALA240 |
| A | ALA241 |
| A | GLY242 |
| A | TRP244 |
| A | HIS263 |
| A | TYR265 |
| A | GLY363 |
| A | PRO364 |
| A | ILE365 |
| A | PHE390 |
| A | TYR392 |
| A | GLY393 |
| A | ILE394 |
| A | ILE395 |
| A | HOH1028 |
| A | HOH1046 |
| A | HOH1120 |
| A | HOH1123 |
| A | HOH1225 |
| site_id | AD3 |
| Number of Residues | 38 |
| Details | binding site for residue FAD B 901 |
| Chain | Residue |
| B | ILE48 |
| B | GLY49 |
| B | GLY51 |
| B | CYS52 |
| B | VAL53 |
| B | LEU72 |
| B | GLU73 |
| B | LYS74 |
| B | GLY80 |
| B | SER81 |
| B | THR82 |
| B | HIS84 |
| B | ALA85 |
| B | ALA86 |
| B | GLY87 |
| B | LEU88 |
| B | PRO211 |
| B | VAL212 |
| B | ALA240 |
| B | ALA241 |
| B | GLY242 |
| B | TRP244 |
| B | HIS263 |
| B | TYR265 |
| B | GLY363 |
| B | PRO364 |
| B | ILE365 |
| B | PHE390 |
| B | TYR392 |
| B | GLY393 |
| B | ILE394 |
| B | ILE395 |
| B | HOH1053 |
| B | HOH1085 |
| B | HOH1108 |
| B | HOH1174 |
| B | HOH1240 |
| B | HOH1290 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24858690, ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB |
| Chain | Residue | Details |
| A | CYS52 | |
| B | PHE390 | |
| A | GLU73 | |
| A | GLY80 | |
| A | VAL212 | |
| A | PHE390 | |
| B | CYS52 | |
| B | GLU73 | |
| B | GLY80 | |
| B | VAL212 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24858690, ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAB |
| Chain | Residue | Details |
| A | TRP244 | |
| B | TRP244 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24858690, ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB |
| Chain | Residue | Details |
| A | GLU573 | |
| A | GLU676 | |
| A | TYR737 | |
| B | GLU573 | |
| B | GLU676 | |
| B | TYR737 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24858690, ECO:0007744|PDB:4PAA |
| Chain | Residue | Details |
| A | TYR669 | |
| B | TYR669 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Tele-8alpha-FAD histidine => ECO:0000269|PubMed:24858690, ECO:0000269|PubMed:4055729, ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB |
| Chain | Residue | Details |
| A | HIS84 | |
| B | HIS84 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9DBT9 |
| Chain | Residue | Details |
| A | LYS107 | |
| B | LYS328 | |
| B | LYS353 | |
| B | LYS757 | |
| A | LYS161 | |
| A | LYS216 | |
| A | LYS328 | |
| A | LYS353 | |
| A | LYS757 | |
| B | LYS107 | |
| B | LYS161 | |
| B | LYS216 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q9DBT9 |
| Chain | Residue | Details |
| A | LYS141 | |
| B | LYS516 | |
| B | LYS648 | |
| B | LYS786 | |
| A | LYS427 | |
| A | LYS469 | |
| A | LYS516 | |
| A | LYS648 | |
| A | LYS786 | |
| B | LYS141 | |
| B | LYS427 | |
| B | LYS469 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9DBT9 |
| Chain | Residue | Details |
| A | LYS310 | |
| A | LYS312 | |
| A | LYS788 | |
| B | LYS310 | |
| B | LYS312 | |
| B | LYS788 |
