Structure of PDB 3qo3 Chain B Binding Site BS01

Receptor Information

>3qo3 Chain B (length=61) Species: 83333 (Escherichia coli K-12)

QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV
YKHAISTVVPS

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 3qo3 Chain A Residue 66

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3qo3 Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): I30 L32
• Binding residue (residue number reindexed from 1): I26 L28
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=6.90,Kd~125nM

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0006355 regulation of DNA-templated transcription

External links

• PDB: RCSB:3qo3, PDBe:3qo3, PDBj:3qo3
• PDBsum: 3qo3
• PubMed: 23226421
• UniProt: P0A6X3|HFQ_ECOLI RNA-binding protein Hfq (Gene Name=hfq)