Structure of PDB 1zbu Chain D Binding Site BS02

Receptor Information
>1zbu Chain D (length=225) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYV
RPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYK
YSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQ
TKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKMHA
GQLMSVSSSLPIEGTPPPQMPHFRK
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 chain1zbu Chain D Residue 4002 [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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PDB1zbu Structural basis for 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease, a human nuclease that also targets siRNA
Resolution2.998 Å
Binding residue
(original residue number in PDB)		E136 A137 C139 N143 F185 W233 F238 H293
Binding residue
(residue number reindexed from 1)		E12 A13 C15 N19 F61 W109 F114 H169
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D134 E136 D234 H293 D298
Catalytic site (residue number reindexed from 1) D10 E12 D110 H169 D174
Enzyme Commision number 3.1.-.-
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0008408 3'-5' exonuclease activity
GO:0019843 rRNA binding
GO:0043022 ribosome binding
GO:0046872 metal ion binding
GO:0071207 histone pre-mRNA stem-loop binding
Biological Process
GO:0000460 maturation of 5.8S rRNA
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:0031047 regulatory ncRNA-mediated gene silencing
GO:0031125 rRNA 3'-end processing
GO:0071044 histone mRNA catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0071204 histone pre-mRNA 3'end processing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1zbu, PDBe:1zbu, PDBj:1zbu
PDBsum1zbu
PubMed
UniProtQ8IV48|ERI1_HUMAN 3'-5' exoribonuclease 1 (Gene Name=ERI1)

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