Structure of PDB 6ogz Chain A Binding Site BS04

Receptor Information
>6ogz Chain A (length=1082) Species: 28875 (Rotavirus A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKYNLILSEYLSFIYNSQSAVQIPIYYSSNSELENRCIEFHSKCLENSKN
GLSLKKLFVEYSDVIENATLLSILSYSYDKYNAVERKLVKYAKGKPLEAD
LTVNELDYENNKITSELFPTAEEYTDLLMDPAILTSLSSNLNAVMFWLEK
HENDVAEKLKIYKRRLDLFTIVASTVNKYGVPRHNAKYRYEYEVMKDKPY
YLVTWANSSIEMLMSVFSHEDYLIARELIVLSYSNRSTLAKLVSSPMSIL
VALVDINGTFITNEELELEFSNKYVRAIVPDQTFDELKQMLDNMRKAGLT
DIPKMIQDWLVDCSIEKFPLMAKIYSWSFHVGFRKQKMLDAALDQLKTEY
TEDVDDEMYREYTMLIRDEVVKMLEEPVKHDDHLLQDSELAGLLSMSSAS
NGESRQLKFGRKTIFSTKKNMHVMDDMANGRYTPGIIPPVNVDKPIPLGR
RDVPGRRTRIIFILPYEYFIAQHAVVEKMLIYAKHTREYAEFYSQSNQLL
SYGDVTRFLSNNSMVLYTDVSQWDSSQHNTQPFRKGIIMGLDMLANMTND
ARVIQTLNLYKQTQINLMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANS
IANLALIKTVLSRISNKYSFATKIIRVDGDDNYAVLQFNTEVTKQMVQDV
SNDVRETYARMNTKVKALVSTVGIEIAKRYIAGGKIFFRAGINLLNNEKK
GQSTQWDQAAVLYSNYIVNRLRGFETDREFILTKIMQMTSVAITGSLRLF
PSERVLTTNSTFKVFDSEDFIIEYGTTDDEVYIQRAFMSLSSQKSGIADE
IAASSTFKNYVSRLSEQLLFSKNNIVSRGIALTEKAKLNSYAPISLEKRR
AQISALLTMLQKPVTFKSSKITINDILRDIKPFFTVNEAHLPIQYQKFMP
TLPDNVQYIIQCIGSRTYQIEDDGSKSAISRLISKYSVYKPSIEELYKVI
SLHENEIQLYLISLGIPKIDADTYVGSKIYSQDKYRILESYVYNLLSINY
GCYQLFDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINHAIKNGSW
ISLFCNYPKSEMIKLWKKMWNITSLRSPYTNA
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 chain6ogz Chain A Residue 1102 [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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PDB6ogz In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		N83 N143 R184 H185 Y189
Binding residue
(residue number reindexed from 1)		N82 N142 R183 H184 Y188
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.48: RNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0019079 viral genome replication
Cellular Component
GO:0044423 virion component

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ogz, PDBe:6ogz, PDBj:6ogz
PDBsum6ogz
PubMed31101900
UniProtG0YZJ9

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