Structure of PDB 8urw Chain Z Binding Site BS03

Receptor Information
>8urw Chain Z (length=1235) Species: 32046 (Synechococcus elongatus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAKSAPIFRNRVIDKKQLKKLIGWTFAHYGTAKTAVVADDLKALGFRYAT
RAGVSISIDDLKVPGSKAELLESAEKRIQETEDRYTRGEITEVERFQKVI
DTWANTNDELTDRVVKNFRESDPLNSVYMMAFSGARGNISQVRQLVGMRG
LMANPQGEIIDLPIKTNFREGLTVTEYIISSYGARKGLVDTALRTADSGY
LTRRLVDVSQDVIIHEVDCGTSRGLFVEAMTDGDRILIPISQRLLGRVTA
EAVLDPSTDEVLAEAGQDINEDLANRIEKAGIKKVKVRSPLTCEAARSVC
QKCYGWSLAHAQMVDMGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGET
ARLLRAPVAGTIKLGKKARTRPYRTRHGEEALLAEANFDLVLEGKGRKET
FAILQGSTIFVQDGDKVAAEAILAEVPVSGRTKRTVEKATKDVATDLAGE
IRFQDIVPEEKTDRQGNTTRIAQRGGLLWVLAGDVYNLLPGAEPTVKNGD
RVEVGDVLAETKLTTERGGTVRMGEDNGSSTHREVEIITASVVLDTATVK
AEASQGREHYVIETKGGQRFNLLAAPGTKVTTGHVVAELIDSRYRTQTGG
LLKYSGVEISKKGRAKAKQGYEVTKGGTLLWIPEETHEVNKDISLLNVED
GQLVEAGTEVVKDIFCQTTGIVSVTQNNDILREIVIKPGDVHVLDDPDTA
AKYDEGRLVNAGEEVFPGLTAEQLVWAEAVDGTDGPLLLLRPVQELVIPD
EPPVPSQDSSQESSSRSIRLRAVQRLQFQDGERIKSVEGVDLLRTQLVLE
SEEGSSQLSADIELLPDSKDPETLRLQLVIIEPVVIRRDVASDTTHGSTH
TELRVKDGQKVKPGAVIACTQIQCKEAGVVRGIQEGSEAVRRLLVERERD
CVTLDLDVTAATQLQPGSLIVAGTQLVDGIIAPESGEVRAIAPGQLQLRI
ARPYRVSQGAVLHVEDKGLVQRGDNLVLLVFERAKTGDIIQGLPRIEELL
EARKPKEACILARRPGVAHINYSDDDAIDIQVIEADGTQADYPVGPGQPL
IISDGETVDAGQALTDGPANPHDLLEIYYDYFREQLGEDYEAALESLRRV
QALLVNEVQSVYQSQGIDISDKHIEVIVRQMTSKVRIDDGGDTIMLPGEL
HELREVYNSNNTMALTGMAPAQFTPVLLGITKASLNTNSFISAASFQETT
RVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFK
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain8urw Chain R 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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PDB8urw Cryo-EM structure of a cyanobacterial RNAP elongation complex with NusG and CTP.
Resolution2.79 Å
Binding residue
(original residue number in PDB)		M339 H343
Binding residue
(residue number reindexed from 1)		M337 H341
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8urw, PDBe:8urw, PDBj:8urw
PDBsum8urw
PubMed38354263
UniProtQ31N15|RPOC2_SYNE7 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC2)

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