Structure of PDB 5x6z Chain C Binding Site BS02

Receptor Information
>5x6z Chain C (length=777) 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
IVSIVGYNPPYVWTCLRHGIRPTYIEKSLPNPGGKGPFGLILPVIHNPQI
KLLCLDTFMLSTSMNILYIGAYPATHLLSLQLNGWTILAFDPKITSDWTD
AMAKATGAKVIGVSKEFDFKSFSVQANQLNMFQNSKLSVIDDTWVETDYE
KFQSEKQAYFEWLIDRTSIDVRLISMKWNRSKDTSVSHLLALLPQPYGAS
IREMRAFFHKKGASDIKILAAETEKYMDDFTAMSVSDQINTQKFMHCMIT
TVGDALKMDLDGGRAVIASYSLSNSSNSKERVLKFLSDANKAKAMVVFGA
PNTHRLAYAKKVGLVLDSAIKMSKDLITFSRDYGYSQSELYDAGYVEITI
DQMVAYSSDVYNGVGYFANSTYNDLFSWYIPKWYVHKRMLMQDIRLSPAA
LVKCFTTLIRNICYVPHETYYRFRGILVDKYLRSKNVDPSQYSIVGSGSK
TFTVLSHFEVPHECGPLVFEASTDVNISGHLLSLAIAAHFVASPMILWAE
QMKYMAVDRMLPPNLDKSLFFDNKVTPSGALQRWHSREEVLLAAEICESY
AAMMLNNKHSPDIIGTLKSAINLVFKI
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5x6z Chain C Residue 902 [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)		D50 M53 E134 V137
Binding residue
(residue number reindexed from 1)		D46 M49 E130 V133
Annotation score3
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

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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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