Structure of PDB 3n2o Chain B Binding Site BS01

Receptor Information
>3n2o Chain B (length=629) Species: 196600 (Vibrio vulnificus YJ016) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDRVRADYNVHYWSQGFYGIDDQGEMYVSPRSDNAHQIQLSKIVKQLEER
QLNVPVLVRFPQILHQRVHSICDAFNQAIEEYQYPNKYLLVYPIKVNQQR
EVVDEILASQAQLETKQLGLEAGSKPELLAVLAMAQHASSVIVCNGYKDR
EYIRLALIGEKLGHKVFIVLEKMSELDLVLREAKSLGVTPRLGIRIRLAS
QGAGKWQASGGEKSKFGLSASQVLNVISRLKKENQLDTLQLVHFHLGSQM
ANIRDVRNGVNESARFYCELRTLGANITYFDVGGGLAIDYDGTRSQSSNS
MNYGLVEYARNIVNTVGDVCKDYKQPMPVIISESGRSLTAHHAVLISNVI
GTETYKPETVTEPEEDFPLLLNNMWRSWLNLHNGTDARALIEIYNDTQSD
LAEVHSQFATGVLTLEHRAWAEQTSLRIYYELNRLMSTKNRFHRPILDEL
SERLADKFFVNFSLFQSLPDSWGIDQVFPVLPLSGLQNAADRRAVMLDIT
CDSDGAIDAYVDGQGIESTLPVPAWNEDEPYLMGFFLVGAYQEILGDMHN
LFGDTHSVVVNVGDQGEINIDFINEGDTVEDMMRYVHIDVDQIRKNYHSL
VSQRVDQEEQQQILAELEQGLSGYTYLED
Ligand information
Ligand IDAG2
InChIInChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChIKeyQYPPJABKJHAVHS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCCNC(N)=N
ACDLabs 10.04[N@H]=C(N)NCCCCN
OpenEye OEToolkits 1.5.0C(CCNC(=N)N)CN
FormulaC5 H14 N4
NameAGMATINE;
(4-AMINOBUTYL)GUANIDINE
ChEMBLCHEMBL58343
DrugBankDB08838
ZINCZINC000001532560
PDB chain3n2o Chain B Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3n2o Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D512 S513
Binding residue
(residue number reindexed from 1)		D502 S503
Annotation score5
Enzymatic activity
Enzyme Commision number 4.1.1.19: arginine decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008792 arginine decarboxylase activity
GO:0016831 carboxy-lyase activity
GO:0046872 metal ion binding
Biological Process
GO:0006527 arginine catabolic process
GO:0008295 spermidine biosynthetic process
GO:0033388 putrescine biosynthetic process from arginine

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3n2o, PDBe:3n2o, PDBj:3n2o
PDBsum3n2o
PubMed20534592
UniProtQ7MK24|SPEA_VIBVY Biosynthetic arginine decarboxylase (Gene Name=speA)

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