Structure of PDB 5lnt Chain B Binding Site BS01

Receptor Information
>5lnt 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]
SPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRA
QGGVARMSDPEMIKEIKNAVTIPVMAKARIGHFVEAQILEAIGVDYVDES
EVLTLADEDNHINKHNFKIPFVCGCRNLGEALRRIREGAAMIRTRGEAGT
GNVVEAVRHVRSVNGAIRLLRSMDDDEVFTYAKKIAAPYDLVVQTKELGR
LPVVQFAAGGVATPADAALMMQLGCDGVFVGSGVFKSGDPVKRAKAIVQA
VTNYRDAAVLAEVSCGLGEAMV
Ligand information
Ligand IDKPR
InChIInChI=1S/C5H10NO5P/c1-4(6)5(7)2-3-11-12(8,9)10/h2-4H,6H2,1H3,(H2,8,9,10)/b3-2+/t4-/m0/s1
InChIKeyRTVKPJRIOVZREZ-ZPYNKGFJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H](N)C(=O)\C=C\O[P](O)(O)=O
OpenEye OEToolkits 2.0.5C[C@@H](C(=O)/C=C/OP(=O)(O)O)N
CACTVS 3.385C[CH](N)C(=O)C=CO[P](O)(O)=O
OpenEye OEToolkits 2.0.5CC(C(=O)C=COP(=O)(O)O)N
FormulaC5 H10 N O5 P
Name[(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate
ChEMBL
DrugBank
ZINCZINC000584905595
PDB chain5lnt 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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PDB5lnt Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Resolution2.32 Å
Binding residue
(original residue number in PDB)		D41 M60 P66 K98 R164 A169 G170 G230 G231 F250 G252 S253
Binding residue
(residue number reindexed from 1)		D20 M39 P45 K77 R143 A148 G149 G209 G210 F229 G231 S232
Annotation score1
Enzymatic activity
Enzyme Commision number 4.3.3.6: pyridoxal 5'-phosphate synthase (glutamine hydrolyzing).
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0036381 pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
GO:0046982 protein heterodimerization activity
Biological Process
GO:0042819 vitamin B6 biosynthetic process
GO:0042823 pyridoxal phosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0009507 chloroplast

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5lnt, PDBe:5lnt, PDBj:5lnt
PDBsum5lnt
PubMed28092359
UniProtO80448|PDX11_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.1 (Gene Name=PDX11)

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