Structure of PDB 4ifd Chain J Binding Site BS03

Receptor Information
>4ifd Chain J (length=948) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQI
VVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCF
FDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFV
ERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKE
VESNIITKSLVQYIELLPNADDIRDSIPQTFSDFTFPEYYSTARVMGGLK
NGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVE
LLPQSEWKAPVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQY
VGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISI
DSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECL
PAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDA
LHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDM
LPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFS
YEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKV
HMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLR
RHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNT
LVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVV
AHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYV
GQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAF
DEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK
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 chain4ifd Chain J Residue 1106 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ifd Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
Resolution2.805 Å
Binding residue
(original residue number in PDB)		C47 C52 C55 H184
Binding residue
(residue number reindexed from 1)		C39 C44 C47 H176
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D543 D549 N551 D552 Y654 R847
Catalytic site (residue number reindexed from 1) D490 D496 N498 D499 Y601 R794
Enzyme Commision number 3.1.13.-
3.1.26.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004519 endonuclease activity
GO:0004521 RNA endonuclease activity
GO:0004527 exonuclease activity
GO:0004540 RNA nuclease activity
GO:0005515 protein binding
Biological Process
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0006401 RNA catabolic process
GO:0016075 rRNA catabolic process
GO:0043628 regulatory ncRNA 3'-end processing
GO:0070651 nonfunctional rRNA decay
GO:0071028 nuclear mRNA surveillance
GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
GO:0071038 TRAMP-dependent tRNA surveillance pathway
GO:0071039 nuclear polyadenylation-dependent CUT catabolic process
Cellular Component
GO:0000176 nuclear exosome (RNase complex)
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ifd, PDBe:4ifd, PDBj:4ifd
PDBsum4ifd
PubMed23376952
UniProtQ08162|RRP44_YEAST Exosome complex exonuclease DIS3 (Gene Name=DIS3)

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