Structure of PDB 5lns Chain B Binding Site BS01

Receptor Information
>5lns Chain B (length=276) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIR
AQGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDE
SEVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAG
TGNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLG
RLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQ
AVTHYSDPEMLVEVSCGLGEAMVGIN
Ligand information
Ligand ID5RP
InChIInChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1
InChIKeyFNZLKVNUWIIPSJ-UHNVWZDZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OCC(=O)[C@H](O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(C(C(=O)CO)O)O)OP(=O)(O)O
CACTVS 3.341OCC(=O)[CH](O)[CH](O)CO[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(=O)CO
OpenEye OEToolkits 1.5.0C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
FormulaC5 H11 O8 P
NameRIBULOSE-5-PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000001532567
PDB chain5lns Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lns Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		D41 P66 K98 V123 A169 G170 G230 G231 G252 S253
Binding residue
(residue number reindexed from 1)		D21 P46 K78 V103 A149 G150 G210 G211 G232 S233
Annotation score2
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:5lns, PDBe:5lns, PDBj:5lns
PDBsum5lns
PubMed28092359
UniProtQ8L940|PDX13_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Gene Name=PDX13)

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