Structure of PDB 3n2o Chain D Binding Site BS01

Receptor Information
>3n2o Chain D (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 IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain3n2o Chain D Residue 1001 [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)		P103 K105 H255 S258 G294 G295 E343 G345 Y551
Binding residue
(residue number reindexed from 1)		P93 K95 H245 S248 G284 G285 E333 G335 Y541
Annotation score1
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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