Structure of PDB 5mc0 Chain B

Receptor sequence

>5mc0B (length=480) Species: 9606 (Homo sapiens)

GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCSRGGMRHSSYTCICGSGENSAVLHY
GHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVY
EAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQ
AHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPG
MVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVV
VTDSGIELLTCVPRTVEEIEACMAGCDKAF

3D structure

• PDB: 5mc0 Structural basis for prolidase deficiency disease mechanisms.
• Chain: B
• Resolution: 1.56 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	B	D286 H369 E411 E451	D281 H364 E406 E446
BS02	MN	B	D275 D286 E451	D270 D281 E446
BS03	GLY	B	D286 H376	D281 H371
BS04	PRO	B	H254 H365 H376 R397 E411 R449	H249 H360 H371 R392 E406 R444

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:5mc0, PDBe:5mc0, PDBj:5mc0
• PDBsum: 5mc0
• PubMed: 30066404
• UniProt: P12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)