Structure of PDB 4ytb Chain A Binding Site BS01

Receptor Information
>4ytb Chain A (length=422) Species: 242619 (Porphyromonas gingivalis W83) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIV
ASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKV
GLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAV
QSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKY
LAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQ
PYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPW
LGTDALHCRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATIS
PVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNS
GRKETYPFIGEPDPFKFTCMNE
Ligand information
Ligand IDGLN
InChIInChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1
InChIKeyZDXPYRJPNDTMRX-VKHMYHEASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC(=O)N)C(C(=O)O)N
OpenEye OEToolkits 1.5.0C(CC(=O)N)[C@@H](C(=O)O)N
ACDLabs 10.04O=C(N)CCC(N)C(=O)O
CACTVS 3.341N[CH](CCC(N)=O)C(O)=O
CACTVS 3.341N[C@@H](CCC(N)=O)C(O)=O
FormulaC5 H10 N2 O3
NameGLUTAMINE
ChEMBLCHEMBL930
DrugBankDB00130
ZINCZINC000001532526
PDB chain4ytb Chain A Residue 503 [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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PDB4ytb Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		W127 D130 R152 Y233 I234 D347 C351
Binding residue
(residue number reindexed from 1)		W84 D87 R109 Y190 I191 D304 C308
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.3.-
Gene Ontology
Molecular Function
GO:0004668 protein-arginine deiminase activity
Biological Process
GO:0009446 putrescine biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:4ytb, PDBe:4ytb, PDBj:4ytb
PDBsum4ytb
PubMed26132828
UniProtQ9RQJ2|PAD_PORGI Peptidylarginine deiminase (Gene Name=PG_1424)

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