Structure of PDB 5lnw Chain D Binding Site BS03

Receptor Information
>5lnw Chain D (length=262) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQ
GGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESE
VLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTG
NIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRL
PVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFPARRARAIVQAVTHYS
DPEMLVEVSCGL
Ligand information
Ligand IDHG3
InChIInChI=1S/C3H9O7P/c4-2(3(5)6)1-10-11(7,8)9/h2-6H,1H2,(H2,7,8,9)/t2-/m1/s1
InChIKeyTWWJQBIRJNUHBT-UWTATZPHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5C(C(C(O)O)O)OP(=O)(O)O
CACTVS 3.385OC(O)[CH](O)CO[P](O)(O)=O
CACTVS 3.385OC(O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 2.0.5C([C@H](C(O)O)O)OP(=O)(O)O
FormulaC3 H9 O7 P
Name[(2~{R})-2,3,3-tris(oxidanyl)propyl] dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5lnw Chain D Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lnw Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H132 R154 R155
Binding residue
(residue number reindexed from 1)		H110 R132 R133
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:5lnw, PDBe:5lnw, PDBj:5lnw
PDBsum5lnw
PubMed28092359
UniProtQ8L940|PDX13_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Gene Name=PDX13)

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