Structure of PDB 5ney Chain D Binding Site BS01

Receptor Information

>5ney Chain D (length=114) Species: 287 (Pseudomonas aeruginosa)

ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVI
GTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDN
DYNDAVVVINWPLG

Ligand information

• Ligand ID: ZDC
• InChI: InChI=1S/C8H14O6/c1-3-6(11)8(13)7(12)4(14-3)2-5(9)10/h3-4,6-8,11-13H,2H2,1H3,(H,9,10)/t3-,4-,6+,7+,8+/m0/s1
• InChIKey: YTZUDUWVQZSKNN-OASCRQMUSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)CC1OC(C(O)C(O)C1O)C
  OpenEye OEToolkits 1.7.6: CC1C(C(C(C(O1)CC(=O)O)O)O)O
  CACTVS 3.370: C[C@@H]1O[C@@H](CC(O)=O)[C@@H](O)[C@H](O)[C@@H]1O
  CACTVS 3.370: C[CH]1O[CH](CC(O)=O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.6: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)CC(=O)O)O)O)O
• Formula: C8 H14 O6
• Name: 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid
• ZINC: ZINC000166514822
• PDB chain: 5ney Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ney Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa.
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): S23 D96 D99 D101 D104
• Binding residue (residue number reindexed from 1): S23 D96 D99 D101 D104
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0044010 single-species biofilm formation

External links

• PDB: RCSB:5ney, PDBe:5ney, PDBj:5ney
• PDBsum: 5ney
• PubMed: 29163899
• UniProt: Q9HYN5