Structure of PDB 2po2 Chain A Binding Site BS01

Receptor Information
>2po2 Chain A (length=236) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYG
PRELHPKHLQRPDRAILRVRYNMAPFSVEERKKPGPDRRSIEISKVIKGA
LEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDL
VAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGYLT
KDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIAQE
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain2po2 Chain A Residue 250 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2po2 Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
Resolution2.41 Å
Binding residue
(original residue number in PDB)		V86 R97 A132 D133 A134 G135 T136 R137 D180
Binding residue
(residue number reindexed from 1)		V78 R89 A124 D125 A126 G127 T128 R129 D172
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.13.-
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0004527 exonuclease activity
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:2po2, PDBe:2po2, PDBj:2po2
PDBsum2po2
PubMed18353775
UniProtQ9V119|RRP41_PYRAB Exosome complex component Rrp41 (Gene Name=rrp41)

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