Structure of PDB 5m4g Chain A Binding Site BS03

Receptor Information
>5m4g Chain A (length=481) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLH
YGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAV
YEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMV
QAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQP
GMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDV
VVTDSGIELLTCVPRTVEEIEACMAGCDKAF
Ligand information
Ligand IDOH
InChIInChI=1S/H2O/h1H2/p-1
InChIKeyXLYOFNOQVPJJNP-UHFFFAOYSA-M
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341
OpenEye OEToolkits 1.5.0		[OH-]
FormulaH O
NameHYDROXIDE ION
ChEMBL
DrugBankDB14522
ZINC
PDB chain5m4g Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5m4g Substrate specificity and reaction mechanism of human prolidase.
Resolution1.48 Å
Binding residue
(original residue number in PDB)		E412 E452
Binding residue
(residue number reindexed from 1)		E407 E447
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D60 H255 D276 D287 H366 H370 H377 R398 E412 Y416 R450 E452
Catalytic site (residue number reindexed from 1) D55 H250 D271 D282 H361 H365 H372 R393 E407 Y411 R445 E447
Enzyme Commision number 3.4.13.9: Xaa-Pro dipeptidase.
Gene Ontology
Molecular Function
GO:0004181 metallocarboxypeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016805 dipeptidase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
GO:0070006 metalloaminopeptidase activity
GO:0102009 proline dipeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0006520 amino acid metabolic process
GO:0030574 collagen catabolic process
GO:0043069 negative regulation of programmed cell death
Cellular Component
GO:0070062 extracellular exosome

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m4g, PDBe:5m4g, PDBj:5m4g
PDBsum5m4g
PubMed28677335
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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