Structure of PDB 2c38 Chain F Binding Site BS01

Receptor Information
>2c38 Chain F (length=241) Species: 2287 (Saccharolobus solfataricus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERPKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAA
VYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELSKVI
REALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPM
RDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMPSLNQVTLFQLNG
SMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEFKEEGV
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain2c38 Chain F Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2c38 Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		T88 R99 A136 S138 R139 E179 D182
Binding residue
(residue number reindexed from 1)		T81 R92 A129 S131 R132 E172 D175
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2c38, PDBe:2c38, PDBj:2c38
PDBsum2c38
PubMed16285928
UniProtQ9UXC2|RRP41_SACS2 Exosome complex component Rrp41 (Gene Name=rrp41)

[Back to BioLiP]