Structure of PDB 5mbz Chain B Binding Site BS03

Receptor Information
>5mbz Chain B (length=478) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKIFSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSCICGSGENSAVLHYAG
APNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVL
RSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLG
AVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLT
VEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDS
GIELLTCVPRTVEEIEACMAGCDKAFTP
Ligand information
Ligand IDGLY
InChIInChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
InChIKeyDHMQDGOQFOQNFH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(=O)O)N
CACTVS 3.341NCC(O)=O
ACDLabs 10.04O=C(O)CN
FormulaC2 H5 N O2
NameGLYCINE
ChEMBLCHEMBL773
DrugBankDB00145
ZINCZINC000004658552
PDB chain5mbz Chain B Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mbz Structural basis for prolidase deficiency disease mechanisms.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		D276 D287 H377
Binding residue
(residue number reindexed from 1)		D266 D277 H367
Annotation score5
Enzymatic activity
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5mbz, PDBe:5mbz, PDBj:5mbz
PDBsum5mbz
PubMed30066404
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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