Structure of PDB 6khp Chain B Binding Site BS02

Receptor Information
>6khp Chain B (length=476) Species: 39947 (Oryza sativa Japonica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFQPLNADDVRSYLHKAVDFISDYYKSVESMPVLPNVKPGYLQDELRASP
PTYSAPFDVTMKELRSSVVPGMTHWASPNFFAFFPSTNSAAAIAGDLIAS
AMNTVGFTWQASPAATEMEVLALDWLAQMLNLPTSFMNRTGEGRGTGGGV
ILGTTSEAMLVTLVAARDAALRRSGSDGVAGLHRLAVYAADQTHSTFFKA
CRLAGFDPANIRSIPTGAETDYGLDPARLLEAMQADADAGLVPTYVCATV
GTTSSNAVDPVGAVADVAARFAAWVHVDAAYAGSACICPEFRHHLDGVER
VDSISMSPHKWLMTCLDCTCLYVRDTHRLGEVTDLKDMQVGVGRRFRGLK
LWMVMRTYGVAKLQEHIRSDVAMAKVFEDLVRGDDRFEVVVPRNFALVCF
RIRAGAGAAAATEEDADEANRELMERLNKTGKAYVAHTVVGGRFVLRFAV
GSSLQEEHHVRSAWELIKKTTTEMMN
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain6khp Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6khp Crystal structure ofOryza sativaTDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis.
Resolution2.299 Å
Binding residue
(original residue number in PDB)		F104 T174 T175 S176 H214 T273 D298 A300 K330
Binding residue
(residue number reindexed from 1)		F84 T154 T155 S156 H194 T253 D278 A280 K310
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.28: aromatic-L-amino-acid decarboxylase.
Gene Ontology
Molecular Function
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0036467 5-hydroxy-L-tryptophan decarboxylase activity
GO:0036469 L-tryptophan decarboxylase activity
Biological Process
GO:0006520 amino acid metabolic process
GO:0006587 serotonin biosynthetic process from tryptophan
GO:0019752 carboxylic acid metabolic process
GO:0042427 serotonin biosynthetic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6khp, PDBe:6khp, PDBj:6khp
PDBsum6khp
PubMed32595985
UniProtQ6ZJK7|TDC1_ORYSJ Tryptophan decarboxylase 1 (Gene Name=TDC1)

[Back to BioLiP]