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Structure of PDB 5lnw Chain D Binding Site BS02

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 ID RP5 InChI InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1 InChIKey KTVPXOYAKDPRHY-TXICZTDVSA-N SMILES Software SMILES CACTVS 3.370 O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O OpenEye OEToolkits 1.7.0 C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)OP(=O)(O)O OpenEye OEToolkits 1.7.0 C(C1C(C(C(O1)O)O)O)OP(=O)(O)O CACTVS 3.370 O[C@@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]1O ACDLabs 12.01 O=P(O)(O)OCC1OC(O)C(O)C1O Formula C5 H11 O8 P Name 5-O-phosphono-beta-D-ribofuranose; [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE; 5-O-phosphono-beta-D-ribose; 5-O-phosphono-D-ribose; 5-O-phosphono-ribose ChEMBL CHEMBL1235722 DrugBank DB04352 ZINC ZINC000004228241 PDB chain 5lnw Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 5lnw Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Resolution 1.9 Å Binding residue (original residue number in PDB) H132 R154 R155 Binding residue (residue number reindexed from 1) H110 R132 R133 Annotation score 1

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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