Structure of PDB 5d4d Chain F Binding Site BS03

Receptor Information

>5d4d Chain F (length=346) Species: 262724 (Thermus thermophilus HB27)

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: 5d4d Chain F Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d4d The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
• Resolution: 3.0 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:5d4d, PDBe:5d4d, PDBj:5d4d
• PDBsum: 5d4d
• PubMed: 27383794
• UniProt: Q5SKW1