Structure of PDB 1ynn Chain D

Receptor sequence

>1ynnD (length=1238) Species: 271 (Thermus aquaticus)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQL
LTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDGV
ALYRFPRRVRVDYLRKERAALRIPLSAWVEKEAYRPGEVLAELSEPYLFR
AEESGVVELKDLAEGHLIYLRQEEEVVARYFLPAGMTPLVVEGEIVEVGQ
PLAEGKGLLRLPRHMTAKEVEAEEEGDSVHLTLFLEWTEPKDYKVAPHMN
VIVPEGAKVQAGEKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP
FEDDVEVTTGDRVAPGDVLADGGKVKSEIYGRVEVDLVRNVVRVVESYDI
DARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRAF
LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN
RLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRS
LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALEL
FKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLL
NRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLS
SFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA
GMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLA
VAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQM
DVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGID
DAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEK
VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGET
FEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVA
HEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLARE
VEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQ
KCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRT

3D structure

• PDB: 1ynn Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase
• Chain: D
• Resolution: 3.3 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	C58 A59	C56 A57
BS02	ZN	D	C1112 C1194 C1204	C1110 C1192 C1202

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• 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

External links

• PDB: RCSB:1ynn, PDBe:1ynn, PDBj:1ynn
• PDBsum: 1ynn
• PubMed: 15692574
• UniProt: Q9KWU6|RPOC_THEAQ DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)