Structure of PDB 6pmd Chain B

Receptor sequence
>6pmdB (length=182) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325) [Search protein sequence]
IPTVIRAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDI
YLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKG
KRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQ
SIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP
3D structure
PDB6pmd Ureadepsipeptides as ClpP Activators.
ChainB
Resolution2.21 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 peptide B L49 A53 T80 H83 L39 A43 T70 H73
BS02 peptide B D27 I29 Y61 Y63 Q89 I91 I93 F113 D17 I19 Y51 Y53 Q79 I81 I83 F103
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6pmd, PDBe:6pmd, PDBj:6pmd
PDBsum6pmd
PubMed31588734
UniProtQ2G036|CLPP_STAA8 ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

[Back to BioLiP]