Structure of PDB 6asg Chain D

Receptor sequence

>6asgD (length=1356) Species: 300852 (Thermus thermophilus HB8)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEV
IAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKV
KSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKEL
LEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPM
VQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEA
VDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSG
RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRML
ERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQ
LHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEP
LAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPI
KVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSP
GRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKT
ARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQA
YEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSG
ARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGA
RKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDE
VTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKA
AEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQ
SIGEPGTQLTQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVF
VESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEA
VERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQ
VLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNT
THVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLK
AIEEAR

3D structure

• PDB: 6asg Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).
• Chain: D
• Resolution: 3.8 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	D	C1112 C1194 C1201 C1204	C985 C1067 C1074 C1077
BS02	MG	D	D739 D741 D743	D612 D614 D616
BS03	ZN	D	C58 C73	C56 C71

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

External links

• PDB: RCSB:6asg, PDBe:6asg, PDBj:6asg
• PDBsum: 6asg
• PubMed: 29606590
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)