Structure of PDB 5yp4 Chain D Binding Site BS01

Receptor Information
>5yp4 Chain D (length=714) Species: 128785 (Pseudoxanthomonas mexicana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEKLTLEAITGSAPLSGPTLTKPQIAPDGSRVTFLRGKDRDRNRLDLWEY
DIASGQTRLLVDSSVVLPGEEVLSDEEKARRERQRIAALSGIVDYQWSPD
GKALLFPLGGELYFYDLTKSGRDAVRKLTNGGGFATDPKISPKGGFVSFI
RDRNLWAIDLASGKEVQLTRDGSDTIGNGVAEFVADEEMDRHTGYWWAPD
DAAIAFARIDETPVPVQKRVEQRYPAAGDHNVRVQLGVIAPKTGARPRWI
DLGKDPDIYLARVDWRDPQRLTFQRQSRDQKKIELIETTLTNGTQRTLVT
ETSTTWVPLHNDLRFLKDGRFLWSSERSGFEHLYVASEDGSTLTALTQGE
WVVDSLLAIDEAAGLAYVSGTRDGATEAHVYAVPLSGGEPRRLTQAPGMH
AATFARNASVFVDSWSSDTTLPQIELFKADGTKLATLLVNDVSDATHPYA
KYRAAHQPTAYGTLTAADGTTPLHYSLIKPAGFDPKKQYPVVVFVYGGPA
AQTVTRAWPGRSDSFFNQYLAQQGYVVFTLDNRGTPRRGAAFGGALYGKQ
GTVEVDDQLRGIEWLKSQAFVDPARIGVYGWSNGGYMTLMLLAKHDEAYA
CGVAGAPVTDWALYDTHYTERYMDLPKANEAGYREASVFTHVDGIGAGKL
LLIHGMADDNVLFTNSTKLMSELQKRGTPFELMTYPGAKHGLRGSDLLHR
YRLTEDFFARCLKP
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain5yp4 Chain D Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yp4 Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E208 E209 Y645
Binding residue
(residue number reindexed from 1)		E187 E188 Y614
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y527 S613 N614 D689 H721
Catalytic site (residue number reindexed from 1) Y496 S582 N583 D658 H690
Enzyme Commision number 3.4.14.5: dipeptidyl-peptidase IV.
Gene Ontology
Molecular Function
GO:0008236 serine-type peptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5yp4, PDBe:5yp4, PDBj:5yp4
PDBsum5yp4
PubMed29426867
UniProtQ6F3I7|DAP4_PSEMX Dipeptidyl aminopeptidase 4 (Gene Name=dap4)

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