Structure of PDB 6r48 Chain B Binding Site BS01

Receptor Information
>6r48 Chain B (length=309) Species: 1111708 (Synechocystis sp. PCC 6803 substr. Kazusa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKPTVIITGASSGVGLYGAKALIDKGWHVIMACRNLDKTQKVADELGFPK
DSYTIIKLDLGYLDSVRRFVAQFRELGRPLKALVCNAAVYFPLLDEPLWS
ADDYELSVATNHLGHFLLCNLLLEDLKACPDADKRLIILGTVTANSKELG
GKIPIPAPPDLGNFEGFEAGFKKPIAMINNKKFKSGKAYKDSKLCNMLTT
RELHRRFHQETGIVFNSLYPGCVADTPLFRNHYSLFRTIFPWFQKNVTKG
YVSQELAGERVAMVVADDKFKDSGVHWSWGQQAGREAFGSDAQKAQRMWD
LSEKLVGLV
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 chain6r48 Chain B Residue 401 [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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PDB6r48 Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		G9 S11 S12 G13 V14 R34 K38 L58 D59 L60 N86 A87 A88 V89 T110 Y189 K193 Y219 V223 T226 L228
Binding residue
(residue number reindexed from 1)		G9 S11 S12 G13 V14 R34 K38 L58 D59 L60 N86 A87 A88 V89 T110 Y189 K193 Y219 V223 T226 L228
Annotation score4
Enzymatic activity
Enzyme Commision number 1.3.1.33: protochlorophyllide reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016630 protochlorophyllide reductase activity
Biological Process
GO:0015979 photosynthesis
GO:0015995 chlorophyll biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6r48, PDBe:6r48, PDBj:6r48
PDBsum6r48
PubMed31645759
UniProtQ59987|POR_SYNY3 Light-dependent protochlorophyllide reductase (Gene Name=por)

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