Structure of PDB 5dkp Chain D

Receptor sequence
>5dkpD (length=191) Species: 122586 (Neisseria meningitidis MC58) [Search protein sequence]
LVPTVIEQSGRGERAFDIYSRLLKERIVFLVGPVTDESANLVVAQLLFLE
SENPDKDIFFYINSPGGSVTAGMSIYDTMNFIKPDVSTLCLGQAASMGAF
LLSAGEKGKRFALPNSRIMIHQPLISGGLGGQASDIEIHARELLKIKEKL
NRLMAKHCDRDLADLERDTDRDNFMSAEEAKEYGLIDQILE
3D structure
PDB5dkp Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity.
ChainD
Resolution2.381 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G73 S102 M103 H127 D178
Catalytic site (residue number reindexed from 1) G67 S96 M97 H121 D172
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 D L28 F65 Y67 L95 L196 L22 F59 Y61 L89 L190
BS02 peptide D L53 S57 F87 L47 S51 F81
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

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Cellular Component
External links
PDB RCSB:5dkp, PDBe:5dkp, PDBj:5dkp
PDBsum5dkp
PubMed26818454
UniProtQ9JZ38|CLPP_NEIMB ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

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