6KHO
Crystal structure of Oryza sativa TDC with PLP
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 | 14 |
| Details | binding site for residue PLP A 601 |
| Chain | Residue |
| A | PHE104 |
| A | LYS330 |
| A | HOH755 |
| A | HOH772 |
| B | VAL380 |
| B | GLY381 |
| A | THR174 |
| A | THR175 |
| A | SER176 |
| A | HIS214 |
| A | GLY271 |
| A | THR273 |
| A | ASP298 |
| A | ALA300 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ACT A 602 |
| Chain | Residue |
| A | TYR359 |
| B | LYS330 |
| B | PLP601 |
| B | ACT602 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue ACT A 603 |
| Chain | Residue |
| A | PHE104 |
| A | PRO105 |
| A | SER106 |
| A | HIS329 |
| A | LYS330 |
| A | HOH915 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue CA A 604 |
| Chain | Residue |
| A | ASP408 |
| A | HOH714 |
| A | HOH717 |
| A | HOH739 |
| A | HOH878 |
| A | HOH910 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue CA A 605 |
| Chain | Residue |
| A | HOH716 |
| A | HOH867 |
| A | HOH925 |
| A | HOH942 |
| B | HOH927 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | binding site for residue PEG A 606 |
| Chain | Residue |
| A | GLN63 |
| A | ASP64 |
| A | LEU66 |
| A | ARG67 |
| A | ALA68 |
| A | PRO71 |
| A | THR72 |
| A | TYR73 |
| A | SER74 |
| B | ARG394 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue PEG A 607 |
| Chain | Residue |
| A | GLN130 |
| A | ASN362 |
| A | HIS363 |
| A | HOH760 |
| A | HOH770 |
| B | TYR472 |
| B | HOH839 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue ACT B 602 |
| Chain | Residue |
| A | ACT602 |
| B | PHE104 |
| B | HIS329 |
| B | LYS330 |
| B | LEU336 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue ACT B 603 |
| Chain | Residue |
| A | PRO357 |
| A | TYR359 |
| B | HIS214 |
| B | SER215 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue CA B 604 |
| Chain | Residue |
| B | ASP408 |
| B | HOH711 |
| B | HOH717 |
| B | HOH770 |
| B | HOH877 |
| B | HOH924 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue CA B 605 |
| Chain | Residue |
| A | HOH763 |
| A | HOH914 |
| B | HOH701 |
| B | HOH890 |
| site_id | AD3 |
| Number of Residues | 22 |
| Details | binding site for Di-peptide PLP B 601 and LYS B 330 |
| Chain | Residue |
| A | VAL380 |
| A | GLY381 |
| A | ACT602 |
| B | PHE104 |
| B | PRO105 |
| B | THR107 |
| B | THR174 |
| B | THR175 |
| B | SER176 |
| B | HIS214 |
| B | THR273 |
| B | ASP298 |
| B | ALA300 |
| B | SER327 |
| B | PRO328 |
| B | HIS329 |
| B | TRP331 |
| B | LEU332 |
| B | ACT602 |
| B | HOH771 |
| B | HOH790 |
| B | HOH886 |
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 |
