Structure of PDB 7jk9 Chain X Binding Site BS01

Receptor Information
>7jk9 Chain X (length=316) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRKGNVVVTGASSGLGLATAKALAETGKWNVIMACRDFLKAERAAKSVGM
PKDSYTVMHLDLASLDSVRQFVDNFRRTETPLDVLVCNAAVYFPTAKEPT
YSAEGFELSVATNHLGHFLLARLLLDDLKKSDYPSKRLIIVGSITGNTNT
LAGNVPPKANLGDLRGLAGGLNGLNSSAMIDGGDFDGAKAYKDSKVCNML
TMQEFHRRFHEETGVTFASLYPGCIASTGLFREHIPLFRALFPPFQKYIT
KGYVSETESGKRLAQVVSDPSLTKSGVYWSWNNASASFENQLSEEASDVE
KARKVWEISEKLVGLA
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain7jk9 Chain X Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7jk9 Photocatalytic LPOR forms helical lattices that shape membranes for chlorophyll synthesis.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		G95 S97 S98 L100 R121 K125 L145 D146 L147 N173 A174 A175 V176 V226 Y276 G308 I310 T313 G314 L315 R317
Binding residue
(residue number reindexed from 1)		G10 S12 S13 L15 R36 K40 L60 D61 L62 N88 A89 A90 V91 V141 Y191 G223 I225 T228 G229 L230 R232
Annotation score4
Enzymatic activity
Enzyme Commision number 1.3.1.33: protochlorophyllide reductase.
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016630 protochlorophyllide reductase activity
GO:0019904 protein domain specific binding
Biological Process
GO:0009723 response to ethylene
GO:0015979 photosynthesis
GO:0015995 chlorophyll biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0009507 chloroplast
GO:0009527 plastid outer membrane
GO:0009534 chloroplast thylakoid
GO:0009535 chloroplast thylakoid membrane
GO:0009579 thylakoid
GO:0009707 chloroplast outer membrane
GO:0009941 chloroplast envelope

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7jk9, PDBe:7jk9, PDBj:7jk9
PDBsum7jk9
PubMed33875834
UniProtP21218|PORB_ARATH Protochlorophyllide reductase B, chloroplastic (Gene Name=PORB)

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