Structure of PDB 1zbh Chain B Binding Site BS02

Receptor Information

>1zbh Chain B (length=225) Species: 9606 (Homo sapiens)

DSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQY
VRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKY
KYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRS
QTKLTIMLEKLGMDYDGRPNCGLDDSKNIARIAVRMLQDGCELRINEKMH
AGQLMSVSSSLPIEGTPPPQMPHFR

Ligand information

• Ligand ID: AMP
• InChI: InChI=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
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 1zbh Chain B Residue 2002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1zbh Structural basis for 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease, a human nuclease that also targets siRNA
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D134 E136 A137 C139 N143 F185 L189 F238
• Binding residue (residue number reindexed from 1): D11 E13 A14 C16 N20 F62 L66 F115
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D134 D234 D298
• Catalytic site (residue number reindexed from 1): D11 D111 D175
• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003676 nucleic acid binding

External links

• PDB: RCSB:1zbh, PDBe:1zbh, PDBj:1zbh
• PDBsum: 1zbh
• UniProt: Q8IV48|ERI1_HUMAN 3'-5' exoribonuclease 1 (Gene Name=ERI1)