Structure of PDB 7mkn Chain D Binding Site BS07

Receptor Information
>7mkn Chain D (length=1340) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFG
PVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAH
IWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEE
QYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETK
RKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATS
DLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG
RAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRL
HQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILD
EVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDG
DQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYM
TRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGEL
VAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILG
LKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAE
IQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQE
EKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANF
REGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDD
CGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTL
LHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGE
AIGVIAAQSIGEPGTQLTAESSIQVKNKGSIKLSNVKSVVNSSGKLVITS
RNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPV
ITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPA
LKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPTG
GLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPY
EEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNE
VQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVK
IANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAA
VAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAG
Ligand information
Ligand ID2TM
InChIInChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
InChIKeySTGUOVSTMBLHFT-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine;
CMPcPP
ChEMBL
DrugBank
ZINCZINC000098208273
PDB chain7mkn Chain T Residue 101 [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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PDB7mkn Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		R425 R731
Binding residue
(residue number reindexed from 1)		R412 R718
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7mkn, PDBe:7mkn, PDBj:7mkn
PDBsum7mkn
PubMed34774797
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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