Structure of PDB 5dkp Chain M Binding Site BS02

Receptor Information
>5dkp Chain M (length=191) Species: 122586 (Neisseria meningitidis MC58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLVPTVIEQSGRGERAFDIYSRLLKERIVFLVGPVTDESANLVVAQLLFL
ESENPDKDIFFYINSPGGSVTAGMSIYDTMNFIKPDVSTLCLGQAASMGA
FLLSAGEKGKRFALPNSRIMIHQPLISGGLGGQASDIEIHARELLKIKEK
LNRLMAKHCDRDLADLERDTDRDNFMSAEEAKEYGLIDQIL
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5dkp Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity.
Resolution2.381 Å
Binding residue
(original residue number in PDB)		L53 S57 F87
Binding residue
(residue number reindexed from 1)		L48 S52 F82
Enzymatic activity
Catalytic site (original residue number in PDB) G73 S102 M103 H127 D178
Catalytic site (residue number reindexed from 1) G68 S97 M98 H122 D173
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
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)

[Back to BioLiP]