Structure of PDB 5x6z Chain B Binding Site BS01

Receptor Information
>5x6z Chain B (length=776) Species: 142805 (Rice dwarf virus (isolate O)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYCIPNFSQTVNERTIIDIFTICRYRSPLVVFCLSHNELAKKYAQDVSMS
SGTHVHIIDGSVEITVSLYRTFRTIATQLLGRMQIVVFVTVDKSVVSTQV
MKSIAWAFRGSFVELRNQSVDSSTLVSKLENLVSFAPLYNVPKCGPDYYG
PTVYSELLSLATNARTHWYATIDYSMFTRSVLTGFVAKYFNEEAVPIDKR
IVSIVGYNPPYVWTCLRHGIRPTYIEKSLPNPGGKGPFGLILPVIMHNPQ
IKLLCLDTFMLSTSMNILYIGAYPATHLLSLQLNGWTILAFDPKITSDWT
DAMAKATGAKVIGVSKEFDFKSFSVQANQLNMFQNSKLSVIDDTWVETDY
EKFQSEKQAYFEWLIDRTSIDVRLISMKWNRSKDTSVSHLLALLPQPYGA
SIREMRAFFHKKGASDIKILAAETEKYMDDFTAMSVSDQINTQKFMHCMI
TTVGDALKMDLDGGRAVIASLSNSSNSKERVLKFLSDANKAKAMVVFGAP
NTHRLAYAKKVGLVLDSAIKMSKDLITFSRDYGYSQSELYDAGYVEITID
QMVAYSSDVYNGVGYFANSTYNDLFSWYIPKWYVHKRMLMQDIRLSPAAL
VKCFTTLIRNICYVPHETYYRFRGILVDKYLRSKNVDPSQYSIVGSGSKT
FTVLSHFEVPHECGPLVFEASTDVNISGHLLSLAIAAHFVASPMILWAEQ
MKYMAVDRMLPPNLDKSLFFDNKVTPSGALQRWHSREEVLLAAEICESYA
AMMLNNKHSPDIIGTLKSAINLVFKI
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain5x6z Chain B Residue 901 [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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PDB5x6z Crystal structure of the capping enzyme P5 from Rice Dwarf Virus
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Q616 Y645 R648 S702 G703 H704 W722 D746 K748 W758 H759
Binding residue
(residue number reindexed from 1)		Q591 Y620 R623 S677 G678 H679 W697 D721 K723 W733 H734
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.50: mRNA guanylyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004484 mRNA guanylyltransferase activity
GO:0005525 GTP binding
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0006370 7-methylguanosine mRNA capping
Cellular Component
GO:0030430 host cell cytoplasm
GO:0044423 virion component

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5x6z, PDBe:5x6z, PDBj:5x6z
PDBsum5x6z
PubMed
UniProtP14583|MCE_RDVA Putative mRNA-capping enzyme P5

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