Structure of PDB 6kqm Chain B Binding Site BS01

Receptor Information

>6kqm Chain B (length=223) Species: 300852 (Thermus thermophilus HB8)

LKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTS
VYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEG
PKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEK
HGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSV
TPLEALNQAVEILREHLTYFSNP

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: 6kqm Chain D Residue 2004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6kqm RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
• Resolution: 3.197 Å
• Binding residue (original residue number in PDB): E154 D168
• Binding residue (residue number reindexed from 1): E149 D163
• 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:6kqm, PDBe:6kqm, PDBj:6kqm
• PDBsum: 6kqm
• PubMed: 32127479
• UniProt: Q5SHR6|RPOA_THET8 DNA-directed RNA polymerase subunit alpha (Gene Name=rpoA)