Structure of PDB 3mkn Chain D Binding Site BS01

Receptor Information
>3mkn Chain D (length=303) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLN
VCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAEST
HAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGG
AYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVI
ARMERAGGPAGELFSDIMNFTLKTQFEGPVHDATCIGYLINPDGIKTQEM
YVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRG
YIK
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 chain3mkn Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mkn Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D11 D16 V124 D240
Binding residue
(residue number reindexed from 1)		D9 D14 V122 D232
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 V122 F163 N164 H231 D232
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: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
Cellular Component
GO:0005829 cytosol

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Cellular Component
External links
PDB RCSB:3mkn, PDBe:3mkn, PDBj:3mkn
PDBsum3mkn
PubMed21082835
UniProtC3T3U2

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