Structure of PDB 5mby Chain A

Receptor sequence

>5mbyA (length=484) Species: 9606 (Homo sapiens)

GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECQVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLH
YGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAV
YEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMV
QAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQP
GMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDV
VVTDSGIELLTCVPRTVEEIEACMAGCDAFTPFS

3D structure

• PDB: 5mby Structural basis for prolidase deficiency disease mechanisms.
• Chain: A
• Resolution: 1.55 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 T410 E412 E452	D282 H365 T405 E407 E447
BS02	MN	A	Y241 D276 D287 E452	Y236 D271 D282 E447
BS03	GLY	A	Y241 D276 D287 H377	Y236 D271 D282 H372
BS04	PRO	A	H255 H366 H377 R398 E412 R450	H250 H361 H372 R393 E407 R445	PDBbind-CN: -logKd/Ki=3.51,Ki=0.31mM

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