Structure of PDB 6woy Chain D Binding Site BS06

Receptor Information
>6woy Chain D (length=1485) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVKRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFR
AEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQ
PLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMN
VVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP
FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDI
DARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAF
LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN
RLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS
LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALEL
FKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLL
NRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLS
SFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA
GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLA
VAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQL
DVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGID
DAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK
VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGET
FEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVT
HEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLARE
VEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ
KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMQGLPRVIELFEARR
PKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGD
YVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKH
IEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAW
KPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVI
LGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA
Ligand information
Ligand IDCH1
InChIInChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-6(13)3-5(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyCHKFLBOLYREYDO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=NC2=O)N)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
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[C@H]2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C[CH]2O
OpenEye OEToolkits 1.5.0C1C(OC(C1O)N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2
FormulaC9 H16 N3 O13 P3
Name3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL480328
DrugBank
ZINCZINC000031440313
PDB chain6woy Chain I 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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PDB6woy The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		R704 P706 R1029
Binding residue
(residue number reindexed from 1)		R702 P704 R1027
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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6woy, PDBe:6woy, PDBj:6woy
PDBsum6woy
PubMed33542236
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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