Structure of PDB 4j6w Chain C Binding Site BS03

Receptor Information

>4j6w Chain C (length=66) Species: 208964 (Pseudomonas aeruginosa PAO1)

HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV
YKHAISTVVPSRPVRL

Ligand information

• Ligand ID: C
• InChI: InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: IERHLVCPSMICTF-XVFCMESISA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
• Formula: C9 H14 N3 O8 P
• Name: CYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL307679
• DrugBank: DB03403
• ZINC: ZINC000003861744
• PDB chain: 4j6w Chain E Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4j6w Hfq binds ribonucleotides in three different RNA-binding sites.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): F42 Y55 H57
• Binding residue (residue number reindexed from 1): F38 Y51 H53
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0006417 regulation of translation
• GO:0009372 quorum sensing
• GO:0043487 regulation of RNA stability
• GO:0043609 regulation of carbon utilization
• GO:0045974 regulation of translation, ncRNA-mediated

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:4j6w, PDBe:4j6w, PDBj:4j6w
• PDBsum: 4j6w
• PubMed: 23897473
• UniProt: Q9HUM0|HFQ_PSEAE RNA-binding protein Hfq (Gene Name=hfq)