Structure of PDB 5lnw Chain B Binding Site BS01

Receptor Information
>5lnw Chain B (length=272) 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
AVTHYSDPEMLVEVSCGLGEAM
Ligand information
Ligand IDK8P
InChIInChI=1S/C8H16NO7P/c1-3-6(10)5(2)9-8(12)7(11)4-16-17(13,14)15/h3,5,7-9,11-12H,1,4H2,2H3,(H2,13,14,15)/t5-,7+,8+/m0/s1
InChIKeyUJGBYPNOGNUCKJ-UIISKDMLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CC(C(=O)C=C)NC(C(COP(=O)(O)O)O)O
CACTVS 3.385C[CH](N[CH](O)[CH](O)CO[P](O)(O)=O)C(=O)C=C
CACTVS 3.385C[C@H](N[C@H](O)[C@H](O)CO[P](O)(O)=O)C(=O)C=C
OpenEye OEToolkits 2.0.5C[C@@H](C(=O)C=C)N[C@@H]([C@@H](COP(=O)(O)O)O)O
FormulaC8 H16 N O7 P
Name[(2~{R},3~{R})-2,3-bis(oxidanyl)-3-[[(2~{S})-3-oxidanylidenepent-4-en-2-yl]amino]propyl] dihydrogen phosphate
ChEMBL
DrugBank
ZINCZINC000584905573
PDB chain5lnw 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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PDB5lnw Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D41 K98 S121 V123 R164 K166 A169 G170 F250 V251 G252 S253
Binding residue
(residue number reindexed from 1)		D21 K78 S101 V103 R144 K146 A149 G150 F230 V231 G232 S233
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:5lnw, PDBe:5lnw, PDBj:5lnw
PDBsum5lnw
PubMed28092359
UniProtQ8L940|PDX13_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Gene Name=PDX13)

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