Structure of PDB 2c39 Chain R Binding Site BS01

Receptor Information
>2c39 Chain R (length=248) Species: 2287 (Saccharolobus solfataricus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREMLQVERPKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMG
NTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRRE
IELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLAL
ADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMPSLNQV
TLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEFKEEGV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2c39 Chain R Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2c39 Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		T88 R99 A134 A136 G137 S138 R139 D182
Binding residue
(residue number reindexed from 1)		T88 R99 A134 A136 G137 S138 R139 D182
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.13.-
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003723 RNA binding
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0016896 RNA exonuclease activity, producing 5'-phosphomonoesters
Biological Process
GO:0006401 RNA catabolic process
GO:0016075 rRNA catabolic process
Cellular Component
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
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:2c39, PDBe:2c39, PDBj:2c39
PDBsum2c39
PubMed16285928
UniProtQ9UXC2|RRP41_SACS2 Exosome complex component Rrp41 (Gene Name=rrp41)

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