Structure of PDB 1yr3 Chain A Binding Site BS01

Receptor Information
>1yr3 Chain A (length=273) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKL
PGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTF
KLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFG
ERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRM
MQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQT
LAAAELSKQNFINLICGFLRKIA
Ligand information
Ligand IDXAN
InChIInChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
InChIKeyLRFVTYWOQMYALW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O=C1NC(=O)c2nc[nH]c2N1
OpenEye OEToolkits 1.5.0c1[nH]c2c(n1)C(=O)NC(=O)N2
ACDLabs 10.04O=C2c1ncnc1NC(=O)N2
FormulaC5 H4 N4 O2
NameXANTHINE
ChEMBLCHEMBL1424
DrugBankDB02134
ZINCZINC000013517187
PDB chain1yr3 Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yr3 Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene
Resolution3.2 Å
Binding residue
(original residue number in PDB)		A118 E197 G214 N239
Binding residue
(residue number reindexed from 1)		A114 E193 G210 N235
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S34 H65 H87 Y89 E90 A117 M215 S216 N239 A241 H251
Catalytic site (residue number reindexed from 1) S30 H61 H83 Y85 E86 A113 M211 S212 N235 A237 H247
Enzyme Commision number 2.4.2.1: purine-nucleoside phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004731 purine-nucleoside phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
GO:0042802 identical protein binding
GO:0047724 inosine nucleosidase activity
GO:0047975 guanosine phosphorylase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006148 inosine catabolic process
GO:0006149 deoxyinosine catabolic process
GO:0006152 purine nucleoside catabolic process
GO:0006161 deoxyguanosine catabolic process
GO:0009116 nucleoside metabolic process
GO:0015949 nucleobase-containing small molecule interconversion
GO:0034214 protein hexamerization
GO:0034355 NAD salvage
GO:0046115 guanosine catabolic process
GO:0055086 nucleobase-containing small molecule metabolic process
GO:1903228 xanthosine catabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yr3, PDBe:1yr3, PDBj:1yr3
PDBsum1yr3
PubMed15808857
UniProtP45563|XAPA_ECOLI Purine nucleoside phosphorylase 2 (Gene Name=xapA)

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