Structure of PDB 5mc4 Chain A

Receptor sequence
>5mc4A (length=465) Species: 9606 (Homo sapiens) [Search protein sequence]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSAPNDRTIQ
NGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMG
AMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGL
GHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFI
DHLLDEALADPARASFLNREVLQRFRGFGRVRIEEDVVVTDSGIELLTCV
PRTVEEIEACMAGCD
3D structure
PDB5mc4 Structural basis for prolidase deficiency disease mechanisms.
ChainA
Resolution1.8 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.4.13.9: Xaa-Pro dipeptidase.
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 MN A D287 H370 E412 E452 D269 H352 E394 E434
BS02 MN A Y241 D276 D287 E452 Y236 D258 D269 E434
BS03 GLY A Y241 D287 H377 Y236 D269 H359
BS04 PRO A H366 H377 R398 E412 H348 H359 R380 E394
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:5mc4, PDBe:5mc4, PDBj:5mc4
PDBsum5mc4
PubMed30066404
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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