Structure of PDB 5uw6 Chain D Binding Site BS02

Receptor Information
>5uw6 Chain D (length=697) Species: 39387 (Gypsophila vaccaria) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGFSKPLHYPPVRRDETVVDDYFGVKVADPYRWLEDPNSEETKEFVDNQE
KLANSVLEECELIDKFKQKIIDFVNFPRCGVPFRRANKYFHFYNSGLQAQ
NVFQMQDDLDGKPEVLYDPNLREGGRSGLSLYSVSEDAKYFAFGIHSGLT
EWVTIKILKTEDRSYLPDTLEWVKFSPAIWTHDNKGFFYCPYPNQEARYH
FLGTDQSEDILLWRDLENPAHHLKCQITDDGKYFLLYILDGCDDANKVYC
LDLTKLPNGLAPFMKLIDSFDASYTAIANDGSVFTFQTNKDAPRKKLVRV
DLNNPSVWTDLVPESKKDLLESAHAVNENQLILRYLSDVKHVLEIRDLES
GALQHRLPIDIGSVDGITARRRDSVVFFKFTSILTPGIVYQCDLKNDPTQ
LKIFRESVVPDFDRSEFEVKQVFVPSKDGTKIPIFIAARKGISLDGSHPC
EMHGYGGFGINMMPTFSASRIVFLKHLGGVFCLANIRGGGEYGEEWHKAG
FRDKKQNVFDDFISAAEYLISSGYTKARRVAIEGGSNGGLLVAACINQRP
DLFGCAEANCGVMDMLRFHKFTLGYLWTGDYGCSDKEEEFKWLIKYSPIH
NVRRPWEQPGNEETQYPATMILTADHDDRVVPLHSFKLLATMQHVLCTSL
EDSPQKNPIIARIQRKAAHYGRATMTQIAEVADRYGFMAKALEAPWI
Ligand information
Ligand IDZPR
InChIInChI=1S/C18H22N2O4/c21-12-15-8-4-10-19(15)17(22)16-9-5-11-20(16)18(23)24-13-14-6-2-1-3-7-14/h1-3,6-7,12,15-16H,4-5,8-11,13H2/t15-,16-/m0/s1
InChIKeyORZXYSPOAVJYRU-HOTGVXAUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)COC(=O)N2CCCC2C(=O)N3CCCC3C=O
CACTVS 3.341O=C[C@@H]1CCCN1C(=O)[C@@H]2CCCN2C(=O)OCc3ccccc3
CACTVS 3.341O=C[CH]1CCCN1C(=O)[CH]2CCCN2C(=O)OCc3ccccc3
OpenEye OEToolkits 1.5.0c1ccc(cc1)COC(=O)N2CCC[C@H]2C(=O)N3CCC[C@H]3C=O
ACDLabs 10.04O=C(N1C(C=O)CCC1)C3N(C(=O)OCc2ccccc2)CCC3
FormulaC18 H22 N2 O4
NameN-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL;
Z-PRO-PROLINAL
ChEMBLCHEMBL79993
DrugBankDB03535
ZINCZINC000003803443
PDB chain5uw6 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5uw6 Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		F178 H239 Y481 F484 S562 W603 R655
Binding residue
(residue number reindexed from 1)		F175 H222 Y455 F458 S536 W577 R629
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H695
Catalytic site (residue number reindexed from 1) H669
Enzyme Commision number 3.4.21.-
3.4.21.26: prolyl oligopeptidase.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0008236 serine-type peptidase activity
GO:0046872 metal ion binding
GO:0070012 oligopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5uw6, PDBe:5uw6, PDBj:5uw6
PDBsum5uw6
PubMed28584123
UniProtR4P353

[Back to BioLiP]