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BioLiP

Structure of PDB 5yp3 Chain D

Receptor sequence
>5yp3D (length=724) Species: 128785 (Pseudoxanthomonas mexicana) [Search protein sequence]
AEKLTLEAITGSAPLSGPTLTKPQIAPDGSRVTFLRGKDRDRNRLDLWEY
DIASGQTRLLVDSSVVLPGEEVLSDEEKARRERQRIAALSGIVDYQWSPD
GKALLFPLGGELYFYDLTKSGRDAVRKLTNGGGFATDPKISPKGGFVSFI
RDRNLWAIDLASGKEVQLTRDGSDTIGNGVAEFVADEEMDRHTGYWWAPD
DAAIAFARIDETPVPVQKRYEVYPDRTEVVEQRYPAAGDHNVRVQLGVIA
PKTGARPRWIDLGKDPDIYLARVDWRDPQRLTFQRQSRDQKKIELIETTL
TNGTQRTLVTETSTTWVPLHNDLRFLKDGRFLWSSERSGFEHLYVASEDG
STLTALTQGEWVVDSLLAIDEAAGLAYVSGTRDGATEAHVYAVPLSGGEP
RRLTQAPGMHAATFARNASVFVDSWSSDTTLPQIELFKADGTKLATLLVN
DVSDATHPYAKYRAAHQPTAYGTLTAADGTTPLHYSLIKPAGFDPKKQYP
VVVFVYGGPAAQTVTRAWPGRSDSFFNQYLAQQGYVVFTLDNRGTPRRGA
AFGGALYGKQGTVEVDDQLRGIEWLKSQAFVDPARIGVYGWSNGGYMTLM
LLAKHDEAYACGVAGAPVTDWALYDTHYTERYMDLPKANEAGYREASVFT
HVDGIGAGKLLLIHGMADDNVLFTNSTKLMSELQKRGTPFELMTYPGAKH
GLRGSDLLHRYRLTEDFFARCLKP
3D structure
PDB5yp3 Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
ChainD
Resolution2.44 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) Y527 S613 N614 D689 H721
Catalytic site (residue number reindexed from 1) Y506 S592 N593 D668 H700
Enzyme Commision number 3.4.14.5: dipeptidyl-peptidase IV.
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 ILE D R106 E208 E209 Y645 R85 E187 E188 Y624
BS02 PRO D Y527 S613 N614 Y649 Y506 S592 N593 Y628
Gene Ontology
Molecular Function
GO:0008236 serine-type peptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:5yp3, PDBe:5yp3, PDBj:5yp3
PDBsum5yp3
PubMed29426867
UniProtQ6F3I7|DAP4_PSEMX Dipeptidyl aminopeptidase 4 (Gene Name=dap4)

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