Structure of PDB 5lnr Chain A Binding Site BS01

Receptor Information
>5lnr Chain A (length=267) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRA
QGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDES
EVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGT
GNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGR
LPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQA
VTHYSDPEMLVEVSCGL
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 chain5lnr Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lnr Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Resolution1.61 Å
Binding residue
(original residue number in PDB)		H132 R147 E151 R154 R155 K166
Binding residue
(residue number reindexed from 1)		H111 R126 E130 R133 R134 K145
Annotation score3
Enzymatic activity
Enzyme Commision number 4.3.3.6: pyridoxal 5'-phosphate synthase (glutamine hydrolyzing).
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0036381 pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
GO:0042803 protein homodimerization activity
GO:0046982 protein heterodimerization activity
Biological Process
GO:0006520 amino acid metabolic process
GO:0006979 response to oxidative stress
GO:0006982 response to lipid hydroperoxide
GO:0009651 response to salt stress
GO:0010224 response to UV-B
GO:0010335 response to non-ionic osmotic stress
GO:0015994 chlorophyll metabolic process
GO:0042538 hyperosmotic salinity response
GO:0042819 vitamin B6 biosynthetic process
GO:0042823 pyridoxal phosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012505 endomembrane system

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5lnr, PDBe:5lnr, PDBj:5lnr
PDBsum5lnr
PubMed28092359
UniProtQ8L940|PDX13_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Gene Name=PDX13)

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