Structure of PDB 5d0w Chain V Binding Site BS01

Receptor Information

>5d0w Chain V (length=226) Species: 559292 (Saccharomyces cerevisiae S288C)

TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAA
DTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIV
AGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEE
AIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQ
KSYKFPRGTTAVLKESIVNICDIQEE

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: 5d0w Chain L Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d0w A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): I163 D166 S169
• Binding residue (residue number reindexed from 1): I163 D166 S169
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): T1 D17 R19 K33 G47 S129 D166 S169
• Catalytic site (residue number reindexed from 1): T1 D17 R19 K33 G47 S129 D166 S169
• Enzyme Commision number: 3.4.25.1: proteasome endopeptidase complex.

Gene Ontology

Molecular Function

• GO:0004298 threonine-type endopeptidase activity

Biological Process

• GO:0051603 proteolysis involved in protein catabolic process

Cellular Component

• GO:0005839 proteasome core complex

External links

• PDB: RCSB:5d0w, PDBe:5d0w, PDBj:5d0w
• PDBsum: 5d0w
• PubMed: 26964885
• UniProt: P25043|PSB2_YEAST Proteasome subunit beta type-2 (Gene Name=PUP1)