Structure of PDB 6byu Chain D Binding Site BS01

Receptor Information
>6byu Chain D (length=1163) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLF
CARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIEL
ASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ
QILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE
TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDG
GRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL
DNGRRGRAITGSNKRPLKSLADMIKGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWD
ILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNAD
FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGL
YYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN
GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYR
ILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRD
GQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIT
ANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVT
EDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPR
NTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIIN
KGEAIGVIAAQSIGEPGTQLTTGGLPRVADLFEARRPKEPAILAEISGIV
SFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDG
PEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRK
ATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKAS
LATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY
AYHQDRMRRRAAG
Ligand information
Ligand IDECJ
InChIInChI=1S/C10H13N5O16P4/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(29-35(25,26)31-33(20,21)22)4(28-10)1-27-34(23,24)30-32(17,18)19/h2-3,10H,1H2,(H,23,24)(H,25,26)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t10-/m1/s1
InChIKeyCDOGMROMDFBAJR-SNVBAGLBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(=O)C(=C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3OC(=C(O[P](O)(=O)O[P](O)(O)=O)C3=O)CO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3C(=O)C(=C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)N
ACDLabs 12.01C(C1=C(OP(O)(=O)OP(O)(O)=O)C(C(O1)n3cnc2c3ncnc2N)=O)OP(OP(O)(=O)O)(=O)O
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3OC(=C(O[P](O)(=O)O[P](O)(O)=O)C3=O)CO[P](O)(=O)O[P](O)(O)=O
FormulaC10 H13 N5 O16 P4
Name(5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate
ChEMBL
DrugBank
ZINC
PDB chain6byu Chain C Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6byu Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		R346 R352 A426 Q465
Binding residue
(residue number reindexed from 1)		R336 R342 A416 Q455
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6byu, PDBe:6byu, PDBj:6byu
PDBsum6byu
PubMed30012465
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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