title: A model of 3D-structure of H+, K+-ATPase catalytic subunit derived by homology modeling.
abstract: OBJECTIVE
  To build a model of 3D-structure of H(+), K(+)-ATPase catalytic subunit for theoretical study and anti-ulcer drug design.
  
  
  METHODS
  The model was built on the basis of structural data from the Ca(2+)-ATPase. Structurally conserved regions were defined by amino acid sequence comparisons, optimum interconnecting loops were selected from the protein databank, and amino (N)- and carboxyl (C)-terminal ends were generated as random coil structures. Applying molecular mechanics method then minimized the model energy. Molecular dynamics technique was used to do further structural optimization.
  
  
  RESULTS
  The model of 3D-structure of H(+), K(+)-ATPase was derived. The model is reasonable according to several validation criteria. There were ten transmembrane helices (TM1-TM10) in the model and inhibitor-binding site was identified on the TM5-8 riched negatively charged residues.
  
  
  CONCLUSIONS
  The 3D-structure model from our study is informative to guide future molecular biology study about H(+), K(+)-ATPase and drug design based on database searching.
authors.affiliation: Shenyang Pharmaceutical University, Shenyang 110016, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Yan
authors.forename: Yuan-dong
authors.initials: YD
authors.lastname: Hu
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.forename: Mao-sheng
authors.initials: MS
authors.lastname: Cheng
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D015195:Drug Design; D017506:H(+)-K(+)-Exchanging ATPase / Q000737:chemistry*; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D017506:H(+)-K(+)-Exchanging ATPase