Structure of PDB 6pmd Chain D Binding Site BS02

Receptor Information

>6pmd Chain D (length=182) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

LIPTVIAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDI
YLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKG
KRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQ
SIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP

Ligand information

>6pmd Chain P (length=7) Species: 32630 (synthetic construct)

tFSPKAK

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pmd Ureadepsipeptides as ClpP Activators.
• Resolution: 2.21 Å
• Binding residue (original residue number in PDB): D27 Y61 Y63
• Binding residue (residue number reindexed from 1): D17 Y51 Y53

Enzymatic activity

• Catalytic site (original residue number in PDB): G69 S98 M99 H123 D172
• Catalytic site (residue number reindexed from 1): G59 S88 M89 H113 D162
• Enzyme Commision number: 3.4.21.92: endopeptidase Clp.

Gene Ontology

Molecular Function

• GO:0004176 ATP-dependent peptidase activity
• GO:0004252 serine-type endopeptidase activity
• GO:0008236 serine-type peptidase activity
• GO:0051117 ATPase binding

Biological Process

• GO:0006508 proteolysis
• GO:0006515 protein quality control for misfolded or incompletely synthesized proteins

Cellular Component

• GO:0005737 cytoplasm
• GO:0009368 endopeptidase Clp complex

External links

• PDB: RCSB:6pmd, PDBe:6pmd, PDBj:6pmd
• PDBsum: 6pmd
• PubMed: 31588734
• UniProt: Q2G036|CLPP_STAA8 ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)