Structure of PDB 5miq Chain A Binding Site BS01

Receptor Information
>5miq Chain A (length=303) Species: 1359 (Lactococcus cremoris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KYDVVIIGSGPAGMTAAMYTARSEMKTLLLERGVPGGQMNNTAEIENYPG
YETIMGPELSMKMAEPLEGLGVENAYGFVTGIEDHGDYKKIITEDDEFIT
KSIIIATGANHRKLEIPGEEEYGARGVSYCAVCDGAFFRNQEILVIGGGD
SAVEEALYLTRFGQSVTIMHRRDKLRAQEIIQQRAFKEEKINFIWDSVPM
EIKGDDKKIQSVVYKNVKTGEVTEKAFGGIFIYVGLDPVAEFVSDLGITD
EAGWIITDDHMRTNIPGIFAVGDVRQKDFRQITTAVGDGAQAAQEAYKFV
VEL
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 chain5miq 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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PDB5miq The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		G12 G14 P15 A16 E35 R36 G41 Q42 T46 N51 V83 T111 G112 E159 V243 G276 D277 Q285 I286
Binding residue
(residue number reindexed from 1)		G8 G10 P11 A12 E31 R32 G37 Q38 T42 N47 V79 T107 G108 E155 V239 G272 D273 Q281 I282
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) V38 P39 M43 E48 C134 C137 D138
Catalytic site (residue number reindexed from 1) V34 P35 M39 E44 C130 C133 D134
Enzyme Commision number 1.8.1.9: thioredoxin-disulfide reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0019430 removal of superoxide radicals
GO:0045454 cell redox homeostasis
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5miq, PDBe:5miq, PDBj:5miq
PDBsum5miq
PubMed28397795
UniProtA2RLJ5

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