Structure of PDB 4xlr Chain J Binding Site BS06

Receptor Information
>4xlr Chain J (length=1367) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQ
LLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDG
VALYRFPRRVRVDYLTEPKDYKVAPHMNVIVPEGAKVQAGEKIVAAIDPE
EEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVTTGDRVAPGDVLADG
GKVKSEIYGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLE
RELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDL
RPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRML
QEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVD
YSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAAR
RMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQ
SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPAS
GEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALN
APIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLE
TSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGM
EKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQI
EQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMA
QSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISS
HGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQ
MDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFL
IKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVV
AAESIGEPGTQLTMTQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGED
RLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPHQLLEA
KGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR
LLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAA
SFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVD
QRTLKAIEEARKEAVEA
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain4xlr Chain J Residue 2003 [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]
PDB4xlr CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		D739 D741 D743
Binding residue
(residue number reindexed from 1)		D615 D617 D619
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: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:4xlr, PDBe:4xlr, PDBj:4xlr
PDBsum4xlr
PubMed26349034
UniProtQ9KWU6|RPOC_THEAQ DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]