Structure of PDB 6vck Chain B Binding Site BS01

Receptor Information

>6vck Chain B (length=160) Species: 83333 (Escherichia coli K-12)

SMIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQA
MYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKW
FLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMK
EFASVVMSLA

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: 6vck Chain B Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vck Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
• Resolution: 2.69 Å
• Binding residue (original residue number in PDB): E53 E120
• Binding residue (residue number reindexed from 1): E54 E121
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.1.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0005515 protein binding
• GO:0016462 pyrophosphatase activity
• GO:0016787 hydrolase activity
• GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
• GO:0034353 mRNA 5'-diphosphatase activity
• GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity

Biological Process

• GO:0006402 mRNA catabolic process
• GO:0008033 tRNA processing
• GO:0050779 RNA destabilization
• GO:0110154 RNA decapping
• GO:0110155 NAD-cap decapping

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6vck, PDBe:6vck, PDBj:6vck
• PDBsum: 6vck
• PubMed: 31960065
• UniProt: P0A776|RPPH_ECOLI RNA pyrophosphohydrolase (Gene Name=rppH)