6KHN
Crystal structure of Oryza sativa TDC with PLP and SEROTONIN
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006520 | biological_process | amino acid metabolic process |
| A | 0006587 | biological_process | serotonin biosynthetic process from tryptophan |
| A | 0016830 | molecular_function | carbon-carbon lyase activity |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0036467 | molecular_function | 5-hydroxy-L-tryptophan decarboxylase activity |
| A | 0036469 | molecular_function | L-tryptophan decarboxylase activity |
| A | 0042427 | biological_process | serotonin biosynthetic process |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006520 | biological_process | amino acid metabolic process |
| B | 0006587 | biological_process | serotonin biosynthetic process from tryptophan |
| B | 0016830 | molecular_function | carbon-carbon lyase activity |
| B | 0016831 | molecular_function | carboxy-lyase activity |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0036467 | molecular_function | 5-hydroxy-L-tryptophan decarboxylase activity |
| B | 0036469 | molecular_function | L-tryptophan decarboxylase activity |
| B | 0042427 | biological_process | serotonin biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | binding site for residue PLP A 601 |
| Chain | Residue |
| A | PHE104 |
| B | VAL380 |
| B | GLY381 |
| A | THR174 |
| A | THR175 |
| A | SER176 |
| A | HIS214 |
| A | GLY271 |
| A | ASP298 |
| A | ALA300 |
| A | LYS330 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue SRO A 602 |
| Chain | Residue |
| A | PHE127 |
| A | TYR359 |
| A | GLY381 |
| B | PHE104 |
| B | PRO105 |
| B | SER106 |
| B | HIS214 |
| B | HIS329 |
| B | LYS330 |
| B | PLP601 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue CA A 603 |
| Chain | Residue |
| A | ASP408 |
| A | HOH701 |
| A | HOH713 |
| A | HOH727 |
| A | HOH734 |
| A | HOH806 |
| A | HOH837 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue CA A 604 |
| Chain | Residue |
| A | HOH852 |
| A | HOH863 |
| A | HOH864 |
| B | HOH859 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | binding site for residue PEG A 605 |
| Chain | Residue |
| A | GLN63 |
| A | ASP64 |
| A | LEU66 |
| A | ALA68 |
| A | PRO71 |
| A | THR72 |
| A | TYR73 |
| A | SER74 |
| A | ALA75 |
| B | ARG394 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | binding site for residue ACT A 606 |
| Chain | Residue |
| A | VAL140 |
| A | ASP144 |
| A | PHE156 |
| A | MET157 |
| A | GLY168 |
| A | GLY169 |
| A | TYR342 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue CA B 602 |
| Chain | Residue |
| B | ASP408 |
| B | HOH718 |
| B | HOH723 |
| B | HOH750 |
| B | HOH788 |
| B | HOH850 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue CA B 603 |
| Chain | Residue |
| A | HOH702 |
| A | HOH781 |
| A | HOH858 |
| A | HOH860 |
| B | HOH711 |
| B | HOH847 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue PEG B 604 |
| Chain | Residue |
| B | GLU310 |
| B | ARG406 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue ACT B 605 |
| Chain | Residue |
| A | PRO357 |
| A | HOH836 |
| B | HIS214 |
| B | SER215 |
| B | HOH765 |
| B | HOH834 |
| site_id | AD2 |
| Number of Residues | 19 |
| Details | binding site for Di-peptide PLP B 601 and LYS B 330 |
| Chain | Residue |
| A | VAL380 |
| A | GLY381 |
| A | SRO602 |
| B | PHE104 |
| B | PRO105 |
| B | THR107 |
| B | THR174 |
| B | THR175 |
| B | SER176 |
| B | THR273 |
| B | ASP298 |
| B | ALA300 |
| B | SER327 |
| B | PRO328 |
| B | HIS329 |
| B | TRP331 |
| B | LEU332 |
| B | HOH726 |
| B | HOH736 |
Functional Information from PROSITE/UniProt
| site_id | PS00392 |
| Number of Residues | 22 |
| Details | DDC_GAD_HDC_YDC DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. SIsMsphKWLmTcLDCtcLYvR |
| Chain | Residue | Details |
| A | SER323-ARG344 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton donor => ECO:0000269|PubMed:32595985 |
| Chain | Residue | Details |
| A | TYR359 | |
| B | TYR359 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:32595985, ECO:0007744|PDB:6KHN |
| Chain | Residue | Details |
| A | PHE104 | |
| A | HIS214 | |
| B | PHE104 | |
| B | HIS214 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:32595985, ECO:0007744|PDB:6KHN, ECO:0007744|PDB:6KHO, ECO:0007744|PDB:6KHP |
| Chain | Residue | Details |
| A | THR175 | |
| A | SER176 | |
| B | THR175 | |
| B | SER176 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P20711 |
| Chain | Residue | Details |
| A | THR273 | |
| B | THR273 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:32595985, ECO:0007744|PDB:6KHP |
| Chain | Residue | Details |
| A | VAL380 | |
| B | VAL380 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:32595985, ECO:0007744|PDB:6KHO |
| Chain | Residue | Details |
| A | GLY381 | |
| B | GLY381 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:32595985, ECO:0007744|PDB:6KHN, ECO:0007744|PDB:6KHP |
| Chain | Residue | Details |
| A | LYS330 | |
| B | LYS330 |
