Structure of PDB 8txo Chain J Binding Site BS06

Receptor Information
>8txo Chain J (length=1162) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFEGAEAIQALLKSMDLEQECEQLRE
ELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV
PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAV
DALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRS
VITVGPYLRLHQCGLPKKMALELFKPFIYGVIREHPVLLNRAPTLHRLGI
QAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALM
MSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAE
RLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVP
KGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAAR
SGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVID
IWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSA
AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLA
DTALKTANSGLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPL
RDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSV
VSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTF
HIGGASSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTK
ESYKVPYGAVLGETVANWDPHTMPGGLPRVADLFEARRPKEPAILAEISG
IVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVIS
DGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQML
RKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITK
ASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGT
GYAYHQDRMRRR
Ligand information
Ligand IDS9F
InChIInChI=1S/C10H17N5O14P3/c11-8-12-9-14(1-2-15(9)10(18)13-8)7-6(17)5(16)4(27-7)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-2,4-7,16-17H,3H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,12,13,18)/q-1/t4-,5-,6-,7-/m1/s1
InChIKeyQAJSSYBGBVOZGX-DBRKOABJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C1=CN(C2=[N-]1C(=O)N=C(N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 2.0.7C1=CN(C2=[N-]1C(=O)N=C(N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385NC1=NC(=O)[N-]2=C(N1)N(C=C2)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.385NC1=NC(=O)[N-]2=C(N1)N(C=C2)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H17 N5 O14 P3
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8txo Chain J Residue 1504 [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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PDB8txo Overcoming resolution attenuation during tilted cryo-EM data collection.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
R425 D462 M932 H936
Binding residue
(residue number reindexed from 1)
R341 D378 M847 H851
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006879 intracellular iron ion homeostasis
GO:0009408 response to heat
GO:0031564 transcription antitermination
GO:0032784 regulation of DNA-templated transcription elongation
GO:0036460 cellular response to cell envelope stress
GO:0042128 nitrate assimilation
GO:0044780 bacterial-type flagellum assembly
GO:0046677 response to antibiotic
GO:0048870 cell motility
GO:0071973 bacterial-type flagellum-dependent cell motility
GO:0090605 submerged biofilm formation
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008023 transcription elongation factor complex
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8txo, PDBe:8txo, PDBj:8txo
PDBsum8txo
PubMed38195598
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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