Structure of PDB 5mc2 Chain A

Receptor sequence

>5mc2A (length=476) Species: 9606 (Homo sapiens)

GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYICGSGENSAVLHYA
PNDRTIQNGDMCLFDMDGEYYCFASDITCSFPANGKFTADQKAVYEAVLR
SSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGA
VFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTV
EPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSG
IELLTCVPRTVEEIEACMAGCDKAFT

3D structure

• PDB: 5mc2 Structural basis for prolidase deficiency disease mechanisms.
• Chain: A
• Resolution: 1.7 Å

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	D276 H359 E401 E441
BS02	GLY	A	D287 H377	D276 H366
BS03	PRO	A	H255 H366 H377 R398 E412 R450	H248 H355 H366 R387 E401 R439

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

External links

• PDB: RCSB:5mc2, PDBe:5mc2, PDBj:5mc2
• PDBsum: 5mc2
• PubMed: 30066404
• UniProt: P12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)