Structure of PDB 5lnr Chain B

Receptor sequence

>5lnrB (length=266) Species: 3702 (Arabidopsis thaliana)

PFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQ
GGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESE
VLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTG
NIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRL
PVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQAV
THYSDPEMLVEVSCGL

3D structure

• PDB: 5lnr Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
• Chain: B
• Resolution: 1.61 Å

Enzymatic activity

• Enzyme Commision number: 4.3.3.6: pyridoxal 5'-phosphate synthase (glutamine hydrolyzing).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	PLP	B	H132 R147 R154 R155 K166	H110 R125 R132 R133 K144

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

External links

• PDB: RCSB:5lnr, PDBe:5lnr, PDBj:5lnr
• PDBsum: 5lnr
• PubMed: 28092359
• UniProt: Q8L940|PDX13_ARATH Pyridoxal 5'-phosphate synthase subunit PDX1.3 (Gene Name=PDX13)