Structure of PDB 5ygq Chain A Binding Site BS01

Receptor Information
>5ygq Chain A (length=341) Species: 258594 (Rhodopseudomonas palustris CGA009) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TETIKTDVLIVGAGPCGLFAVFELGLLDVKAHLVDILDKVGGQCAELYPE
KPIYDIPGIPMVTGHGLTEALMEQIKPFNPTFHLSEMVENVEKIGDPGFR
VTTNAGKVFECTVLVVAAGGGSFLPKRPPVPGVEAYEGTSVHYAVRKMED
FRGKDILIVGGGDSALDWTLNLNPIAKSMTLVHRRDDFRGAPHSVEQMRQ
LVASGKLDLKIGQITELQGDNGQLTGATVKLNDNTTSQIKCDAMLPFFGL
TMKLGPVANWGLDLENNLIPVDTGTFETNVPGIFAIGDINTYPGKLKLIL
SGFHEGALMAQKAVKYVYPDKRVVFQYTTSSTNLQKKLGVN
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain5ygq Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ygq Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP+oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP+/NADPH.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		V12 G15 P16 C17 D36 I37 Q44 Y49 I54 D56 M88 V89 A119 G120 G122 S123 F124 G288 D289 I300
Binding residue
(residue number reindexed from 1)		V11 G14 P15 C16 D35 I36 Q43 Y48 I53 D55 M87 V88 A118 G119 G121 S122 F123 G287 D288 I299
Annotation score2
Enzymatic activity
Enzyme Commision number 1.18.1.2: ferredoxin--NADP(+) reductase.
Gene Ontology
Molecular Function
GO:0004324 ferredoxin-NADP+ reductase activity
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0050661 NADP binding
Biological Process
GO:0045454 cell redox homeostasis
GO:0098869 cellular oxidant detoxification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ygq, PDBe:5ygq, PDBj:5ygq
PDBsum5ygq
PubMed31838096
UniProtQ6N2U4|FENR_RHOPA Ferredoxin--NADP reductase (Gene Name=RPA3954)

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