Structure of PDB 5mc3 Chain B Binding Site BS02

Receptor Information
>5mc3 Chain B (length=484) 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
GMVLTVKPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDV
VVTDSGIELLTCVPRTVEEIEACMAGCDKAFTPF
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 chain5mc3 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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PDB5mc3 Structural basis for prolidase deficiency disease mechanisms.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		Y241 H255 H377 K412
Binding residue
(residue number reindexed from 1)		Y236 H250 H372 K407
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:5mc3, PDBe:5mc3, PDBj:5mc3
PDBsum5mc3
PubMed30066404
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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