Structure of PDB 5jwg Chain A Binding Site BS01

Receptor Information
>5jwg Chain A (length=703) Species: 28124 (Porphyromonas endodontalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDGGMWLMQQINGQVARMKSLGMQLEAADIYNPNGSSLKDAVVMFDGGCT
GVLVSNQGLLLTNHHCGYDQIQKHSSVQHNYLKDGFWSYSLAEELVNPGL
EVEIVDEITDVTAAVKKELERIKKPSGLEFLSPRYLSSLAPEIVGKKAAS
RPGYRYEIKAFYGGNRYYMFTKKVFRDVRLVAAPPSSIGKFGSDTDNWAW
PRHTGDFSIFRLYADKNGNPAEYSKDNVPYRPKRWVKVNAQGVKEGDFAL
IMGYPGTTYKFFTADEVTEWSEIDNNIRIEMRGILQDVMLREMLADPKIN
IMYAAKYASSQNGYKRAQGANWAIRRRSLREIKLAQQQEVLAWAKQKGIA
TTEEAVRAISKAIEGRQDLRMRQRYLLEGILMGIEMSNAPAADSDIADHW
DDPARREAGLQSIRKQFEAFFNKDYSPEVEKDQLAIALLTRYAERIPAEK
QPISIREGIAEYGSAKAYVEMIFDKSIYASRERFEEFMKNPDRDRLLRDP
MSRFAASVAYEHQKLAKEVAAFDAPLAAAQRSYVASVLDMKGQPNLAPDA
NLTLRFTYGEIKGYQPRDVVTYGAKSTLEGVMEKEDPNNWEYVVDPKLKA
LYEAKNYGRYANSDGSMPVNFCATTHTTGGNAGSPVMNARGELIGLNFDR
NWEGVGGDIEYLPNYQRSIILDIRYLLFIIDKFAGCQRLIDEIQPQFHHH
HHH
Ligand information
Ligand IDARG
InChIInChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
InChIKeyODKSFYDXXFIFQN-BYPYZUCNSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC(C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[C@@H](CCCNC(N)=[NH2+])C(O)=O
OpenEye OEToolkits 1.5.0C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[CH](CCCNC(N)=[NH2+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCN\C(=[NH2+])N
FormulaC6 H15 N4 O2
NameARGININE
ChEMBL
DrugBank
ZINC
PDB chain5jwg Chain A 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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PDB5jwg Bacterial protease uses distinct thermodynamic signatures for substrate recognition.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H85 N217 W218 N332 D669
Binding residue
(residue number reindexed from 1)		H65 N197 W198 N312 D649
Annotation score4
Enzymatic activity
Enzyme Commision number 3.4.14.-
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0008236 serine-type peptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0070009 serine-type aminopeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0043171 peptide catabolic process
Cellular Component
GO:0005576 extracellular region
GO:0009986 cell surface

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5jwg, PDBe:5jwg, PDBj:5jwg
PDBsum5jwg
PubMed28588213
UniProtF8WQK8|DPP11_POREA Asp/Glu-specific dipeptidyl-peptidase (Gene Name=dpp11)

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