Structure of PDB 6kqd Chain F Binding Site BS02

Receptor Information

>6kqd Chain F (length=346) Species: 300852 (Thermus thermophilus HB8)

SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLI
REVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIA
REGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF
EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ
LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDS
FYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID
GREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 6kqd Chain F Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6kqd RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): A292 G296 W299
• Binding residue (residue number reindexed from 1): A215 G219 W222
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003700 DNA-binding transcription factor activity
• GO:0016987 sigma factor activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006352 DNA-templated transcription initiation
• GO:0006355 regulation of DNA-templated transcription
• GO:0010468 regulation of gene expression
• GO:2000142 regulation of DNA-templated transcription initiation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6kqd, PDBe:6kqd, PDBj:6kqd
• PDBsum: 6kqd
• PubMed: 32127479
• UniProt: Q5SKW1