Structure of PDB 3b9x Chain D Binding Site BS01

Receptor Information
>3b9x Chain D (length=307) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLN
VCQKLEINVPVYAGMPQPIMRQQIVAIHGDTGLDGPVFEPLTRQAESTHA
VKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAY
GTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIAR
MERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIK
TQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEE
CVRGYIK
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain3b9x Chain D Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3b9x Structural basis for substrate specificity in group I nucleoside hydrolases
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D11 D16 V124 D240
Binding residue
(residue number reindexed from 1)		D9 D14 V120 D236
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D11 D16 N40 Q75 V124 F165 N166 H239 D240
Catalytic site (residue number reindexed from 1) D9 D14 N38 Q73 V120 F161 N162 H235 D236
Enzyme Commision number 3.2.2.8: ribosylpyrimidine nucleosidase.
Gene Ontology
Molecular Function
GO:0005509 calcium ion binding
GO:0008477 purine nucleosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0042802 identical protein binding
GO:0045437 uridine nucleosidase activity
GO:0046872 metal ion binding
GO:0050263 ribosylpyrimidine nucleosidase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006152 purine nucleoside catabolic process
GO:0006206 pyrimidine nucleobase metabolic process
GO:0046133 pyrimidine ribonucleoside catabolic process
GO:0051289 protein homotetramerization
Cellular Component
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Biological Process
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Cellular Component
External links
PDB RCSB:3b9x, PDBe:3b9x, PDBj:3b9x
PDBsum3b9x
PubMed18361502
UniProtP33022|RIHB_ECOLI Pyrimidine-specific ribonucleoside hydrolase RihB (Gene Name=rihB)

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