Structure of PDB 5lnv Chain C Binding Site BS02

Receptor Information
>5lnv Chain C (length=276) 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
VTHYSDPEMLVEVSCGLGEAMVGINL
Ligand information
Ligand IDKIK
InChIInChI=1S/C5H9NO2/c1-2-5(8)4(6)3-7/h2,4,7H,1,3,6H2/t4-/m0/s1
InChIKeyUCJPATVGPSMUQX-BYPYZUCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5C=CC(=O)[C@H](CO)N
OpenEye OEToolkits 2.0.5C=CC(=O)C(CO)N
CACTVS 3.385N[C@@H](CO)C(=O)C=C
CACTVS 3.385N[CH](CO)C(=O)C=C
FormulaC5 H9 N O2
Name(4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one
ChEMBL
DrugBank
ZINCZINC000116725649
PDB chain5lnv Chain C Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lnv Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Resolution2.24 Å
Binding residue
(original residue number in PDB)		K98 V123 R164 K166
Binding residue
(residue number reindexed from 1)		K77 V102 R143 K145
Annotation score1
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:5lnv, PDBe:5lnv, PDBj:5lnv
PDBsum5lnv
PubMed28092359
UniProtQ8L940|PDX13_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Gene Name=PDX13)

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