Structure of PDB 5d4d Chain L Binding Site BS01

Receptor Information

>5d4d Chain L (length=222) Species: 274 (Thermus thermophilus)

LKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTS
VYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLPSLQTVTLLLKAEGP
KEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKH
GIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVT
PLEALNQAVEILREHLTYFSNP

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 L 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): D183 D193
• Binding residue (residue number reindexed from 1): D177 D187
• Annotation score: 1

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046983 protein dimerization activity

Biological Process

• GO:0006351 DNA-templated transcription

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005737 cytoplasm

External links

• PDB: RCSB:5d4d, PDBe:5d4d, PDBj:5d4d
• PDBsum: 5d4d
• PubMed: 27383794
• UniProt: Q5SHR6|RPOA_THET8 DNA-directed RNA polymerase subunit alpha (Gene Name=rpoA)