Structure of PDB 3b0v Chain D Binding Site BS02

Receptor Information
>3b0v Chain D (length=315) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERL
LAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQE
GGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSV
EAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTF
VTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPS
RLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGR
SLQALDRALRLMEEE
Ligand information
Ligand IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain3b0v Chain D Residue 400 [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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PDB3b0v Molecular basis of dihydrouridine formation on tRNA
Resolution3.51 Å
Binding residue
(original residue number in PDB)		P10 M11 V12 M36 Q63 N90 K132 H164 R178 N203 G225 R226
Binding residue
(residue number reindexed from 1)		P10 M11 V12 M36 Q63 N90 K132 H164 R178 N203 G225 R226
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.1.-
1.3.1.91: tRNA-dihydrouridine(20) synthase [NAD(P)(+)].
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0017150 tRNA dihydrouridine synthase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0102264 tRNA-dihydrouridine20 synthase activity
GO:0102266 tRNA-dihydrouridine20a synthase activity
Biological Process
GO:0002943 tRNA dihydrouridine synthesis
GO:0008033 tRNA processing

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3b0v, PDBe:3b0v, PDBj:3b0v
PDBsum3b0v
PubMed22123979
UniProtQ5SMC7|DUSAL_THET8 tRNA-dihydrouridine(20/20a) synthase (Gene Name=dus)

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