Structure of PDB 6srg Chain B

Receptor sequence

>6srgB (length=468) Species: 9606 (Homo sapiens)

GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLKIHSK
EHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFD
GISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVK
VGMKEYELESLFEHYCYSRGGMRHSSYTCICAVLHYGHAGAPNDRTIQNG
DMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAM
KPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGH
FLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDH
LLDEALADPARASFLNREVLQRFRGFGRVRIEEDVVVTDSGIELLTCVPR
TVEEIEACMAGCDKAFTP

3D structure

• PDB: 6srg Co-expression with chaperones can affect protein 3D structure as exemplified by loss-of-function variants of human prolidase.
• Chain: B
• Resolution: 2.558 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	D287 H370 E412 E452	D267 H350 E392 E432
BS02	MN	B	Y241 D276 D287 E452	Y227 D256 D267 E432
BS03	GLY	B	Y241 D287 H377	Y227 D267 H357
BS04	PRO	B	H366 H377 R398	H346 H357 R378

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:6srg, PDBe:6srg, PDBj:6srg
• PDBsum: 6srg
• PubMed: 32598484
• UniProt: P12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)