Structure of PDB 3jb6 Chain A Binding Site BS03

Receptor Information
>3jb6 Chain A (length=1196) Species: 110829 (Bombyx mori cypovirus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKLHNTIFSETRKFTRESFKEIEHLTARLANDRVARHDFLFNTSIVLISD
YSGEDSNGNQLQATITIPNEIINPKEYDPSDYPLAEDESFFKQGHKYDYL
VTFRAGSLTNTYEPKTKMYKLHAALDKLMHVKQRKSRFADLWRELCAVIA
SLDVWYQTTNYPLRTYVKLLFHKGDEFPFYESPSQDRIIFNDKSVASILP
TFVYTCCQVGTAIMSGILTHVESIVAMNHFLHCAKDSYIDEKLKIKGIGR
SWYQEALHNVCQATVPVWSQFNEVIGHRTKSTSEPHFVSSTFISLRAKRA
ELLYPEFNAYINRAIQLSKTQNDVANYYAACRAMTNDGTFLATLTELSLD
AAVFPRIEQHLVTRPAVLMSNTRHESLKQKYTNGVGSIAQSYLSSFTDEI
AKRVNGRHHDEAWLNFLTTSRIVMQAVFAREYRTPERIFKSLKAPIKLVE
RQQSDRRQRAISGLDNDRLFLSFMPYTIGKQIYELNDNAAQGKQAGNAFD
IGEMLYWTSQRNVLLSSIDVAGMDASVTTNTKDIYNTFVLDVASKCTVPR
FGPYYAKNMEVFEAGNRQSQVRYVNAAWQACALEAANSQTSTSYESEIFG
QVKNAEGTYPSGRADTSTHHTVLLQGLVRGNELKRASDGKNSCLATIKIL
GDDIMEIFQGSESDTYDHAVSNASILNESGFATTAELSQNSIVLLQQLVV
NGTFWGFADRISLWTREDTKDIGRLNLAMMELNALIDDLVFRVRRPEGLK
MLGFFCGAICLRRFTLSVDNKLYDSTYNNLSKYMTLTKYDKNPDSDSTLM
SLILPLAWLFMPRGGEYPAYPFERRDGTFTEDESMFTARGAYKRRLLYDV
SNIGEMIQQNSMALDDDLLHEYGFTGALLLIDLNILDLIDEVKKEDISPV
KVSELATSLEQLGKLGEREKSRRAASDLKIRGHALSNDIVYGYGLQEKIQ
KSAMATKETTVQSKRVSSRLHDVIVAKTRDYKISTIPADALHLHEFEVED
VTVDLLPHAKHTSYSSLAYNMSFGSDGWFAFALLGGLDRSANLLRLDVAS
IRGNYHKFSYDDPVFKQGYKIYKSDATLLNDFFTAISAGPKEQGILLRAF
AYYSLYGNVEYHYVLSPRQLFFLSDNPVSAERLVRIPPKYYVSTQCRALY
NIFSYLHILRSIANNRGKRLKMVLHPGLIAYVRGTSQGAILPEADN
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 chain3jb6 Chain A Residue 1301 [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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PDB3jb6 In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		R37 D144 R147 Y184
Binding residue
(residue number reindexed from 1)		R33 D140 R143 Y180
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.48: RNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
Biological Process
GO:0001172 RNA-templated transcription
GO:0019079 viral genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3jb6, PDBe:3jb6, PDBj:3jb6
PDBsum3jb6
PubMed26503045
UniProtD0EZK6

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