Structure of PDB 3wod Chain D Binding Site BS01

Receptor Information
>3wod Chain D (length=1488) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLF
RAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKG
QPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHM
NVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVY
PFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYD
IDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRA
FLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRN
NRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLR
SLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALE
LFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVL
LNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPL
SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG
AGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALL
AVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQ
LDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGI
DDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTE
KVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGE
TFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDV
THEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAR
EVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVC
QKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMGLPRVIELFEARR
PKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGD
YVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKH
IEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAW
KPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVI
LGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain3wod Chain D Residue 1601 [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]
PDB3wod Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		C1194 C1204
Binding residue
(residue number reindexed from 1)		C1193 C1203
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:3wod, PDBe:3wod, PDBj:3wod
PDBsum3wod
PubMed24589779
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]