Structure of PDB 6ye8 Chain B Binding Site BS03

Receptor Information

>6ye8 Chain B (length=340) Species: 83333 (Escherichia coli K-12)

QKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTG
FDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNK
FAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVS
FLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQ
YINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFD
VFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAE
VRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKS

Ligand information

• Ligand ID: JFN
• InChI: InChI=1S/C4H11NO/c1-4(5)3-6-2/h4H,3,5H2,1-2H3/t4-/m1/s1
• InChIKey: NXMXETCTWNXSFG-SCSAIBSYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(COC)N
  CACTVS 3.385: COC[C@@H](C)N
  CACTVS 3.385: COC[CH](C)N
  OpenEye OEToolkits 2.0.6: C[C@H](COC)N
  ACDLabs 12.01: COCC(C)N
• Formula: C4 H11 N O
• Name: (2R)-1-methoxypropan-2-amine;
  jeffamine
• ZINC: ZINC000004862149
• PDB chain: 6ye8 Chain B Residue 405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ye8 A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): R357 R361
• Binding residue (residue number reindexed from 1): R329 R333
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0019808 polyamine binding
• GO:0019810 putrescine binding

Biological Process

• GO:0015846 polyamine transport
• GO:0015847 putrescine transport

Cellular Component

• GO:0016020 membrane
• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space
• GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing

External links

• PDB: RCSB:6ye8, PDBe:6ye8, PDBj:6ye8
• PDBsum: 6ye8
• PubMed: 33406388
• UniProt: P31133|POTF_ECOLI Putrescine-binding periplasmic protein PotF (Gene Name=potF)