Structure of PDB 1yt3 Chain A Binding Site BS01

Receptor Information
>1yt3 Chain A (length=375) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGE
HLALIDPLGITDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPL
IDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCE
YAAADVWYLLPITAKLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAW
RDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWSVARY
MPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDM
PGYRKAFKAIKSLITDVSETHKISAELLASRRQINQLLNWHWKLKPQNNL
PELISGWRGELMAEALHNLLQEYPQ
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain1yt3 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yt3 Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing
Resolution1.6 Å
Binding residue
(original residue number in PDB)		D28 E30 D155
Binding residue
(residue number reindexed from 1)		D28 E30 D155
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D28 E30 D85 Y151 D155
Catalytic site (residue number reindexed from 1) D28 E30 D85 Y151 D155
Enzyme Commision number 3.1.13.5: ribonuclease D.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0004527 exonuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0033890 ribonuclease D activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0008033 tRNA processing
GO:0042780 tRNA 3'-end processing
GO:0044237 cellular metabolic 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:1yt3, PDBe:1yt3, PDBj:1yt3
PDBsum1yt3
PubMed16004870
UniProtP09155|RND_ECOLI Ribonuclease D (Gene Name=rnd)

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