Structure of PDB 4jk2 Chain D Binding Site BS03

Receptor Information
>4jk2 Chain D (length=1160) 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
DNGRRGRAITGSNKRPLKSLADMIKGGKRVDYSGRSVITVGPYLRLHQCG
LPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIR
EHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMA
VHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDC
VNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKT
SLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPT
VIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQ
FQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQV
SFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGL
NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTH
EGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQ
WCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGV
IAAQSIGEPGTQLTMRDITGGLPRVADLFEARRPKEPAILAEISGIVSFG
KETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEA
PHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATI
VNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLAT
ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYH
QDRMRRRAAG
Ligand information
Ligand ID0O2
InChIInChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyKCPMACXZAITQAX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=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[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H18 N5 O20 P5
Nameguanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
ChEMBL
DrugBank
ZINCZINC000083923877
PDB chain4jk2 Chain D Residue 1503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4jk2 Differential regulation by ppGpp versus pppGpp in Escherichia coli.
Resolution4.201 Å
Binding residue
(original residue number in PDB)		R362 K615 I619 D622
Binding residue
(residue number reindexed from 1)		R345 K598 I602 D605
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:4jk2, PDBe:4jk2, PDBj:4jk2
PDBsum4jk2
PubMed23620295
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]