Structure of PDB 5xj0 Chain D Binding Site BS01

Receptor Information
>5xj0 Chain D (length=1462) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVL
YFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDA
LVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPL
AAWVEKEAYKPGEILAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDE
PVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVEAEEE
GETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEV
IAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKV
KSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKEL
LEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPM
VQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEA
VDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSG
RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRML
ERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQ
LHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEP
LAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPI
KVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSP
GRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKT
ARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQA
YEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSG
ARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGA
RKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDE
VTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKA
AEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQ
SIGEPGTQLTMGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVF
VESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEA
VERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQ
VLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNT
THVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLK
AIEEARKEAVEA
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 chain5xj0 Chain D Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xj0 A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation
Resolution4.004 Å
Binding residue
(original residue number in PDB)		C1194 C1201 C1204
Binding residue
(residue number reindexed from 1)		C1167 C1174 C1177
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5xj0, PDBe:5xj0, PDBj:5xj0
PDBsum5xj0
PubMed29165680
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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