Structure of PDB 5mbz Chain A

Receptor sequence
>5mbzA (length=481) Species: 9606 (Homo sapiens) [Search protein sequence]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKIFSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSICGSGENSAVLHYGH
AGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEA
VLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAH
LGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMV
LTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVT
DSGIELLTCVPRTVEEIEACMAGCDKAFTPF
3D structure
PDB5mbz Structural basis for prolidase deficiency disease mechanisms.
ChainA
Resolution1.5 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 D279 H362 T402 E404 E444
BS02 MN A D276 D287 E452 D268 D279 E444
BS03 GLY A D287 H377 D279 H369
BS04 PRO A H255 H366 H377 R398 E412 H247 H358 H369 R390 E404
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5mbz, PDBe:5mbz, PDBj:5mbz
PDBsum5mbz
PubMed30066404
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

[Back to BioLiP]