Structure of PDB 2pnz Chain B Binding Site BS01

Receptor Information
>2pnz Chain B (length=267) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGST
QVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTFEPGPPDERAIELA
RVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAA
IAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIGNILVV
DPSLDEELVMDGKITITTDETGHISAVQKSEGGAFKLEEVMYAVETAFKK
AEEIRKLILEAVEKAKQ
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain2pnz Chain A Residue 279 [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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PDB2pnz Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
Resolution2.14 Å
Binding residue
(original residue number in PDB)		E69 T81 F137
Binding residue
(residue number reindexed from 1)		E62 T74 F130
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.13.-
Gene Ontology
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

View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2pnz, PDBe:2pnz, PDBj:2pnz
PDBsum2pnz
PubMed18353775
UniProtQ9V118|RRP42_PYRAB Exosome complex component Rrp42 (Gene Name=rrp42)

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