Structure of PDB 6dt4 Chain B Binding Site BS01

Receptor Information

>6dt4 Chain B (length=200) Species: 214092 (Yersinia pestis CO92)

DPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGK
EMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQ
VNPDILMRLSSQMANRLQITSEKVGNLAFLDVTGRIAQTLLNLAKQPDAM
THPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG

Ligand information

• Ligand ID: CMP
• InChI: InChI=1S/C10H12N5O6P/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(20-10)1-19-22(17,18)21-7/h2-4,6-7,10,16H,1H2,(H,17,18)(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
• InChIKey: IVOMOUWHDPKRLL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(O4)O)O)N
  ACDLabs 10.04: O=P3(OCC4OC(n1c2ncnc(N)c2nc1)C(O)C4O3)O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@](=O)(O4)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]4[C@H]3O
• Formula: C10 H12 N5 O6 P
• Name: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE;
  CYCLIC AMP;
  CAMP
• ChEMBL: CHEMBL316966
• DrugBank: DB02527
• ZINC: ZINC000003873977
• PDB chain: 6dt4 Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dt4 The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): V50 I71 G72 E73 L74 R83 S84 A85 R124
• Binding residue (residue number reindexed from 1): V42 I63 G64 E65 L66 R75 S76 A77 R116
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003700 DNA-binding transcription factor activity

Biological Process

• GO:0006355 regulation of DNA-templated transcription

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6dt4, PDBe:6dt4, PDBj:6dt4
• PDBsum: 6dt4
• PubMed: 31744922
• UniProt: A0A2U2GZI4