5ER2

High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. the analysis of the inhibitor binding and description of the rigid body shift in the enzyme

5ER2 の概要

• エントリーDOI: 10.2210/pdb5er2/pdb
• 関連するBIRD辞書のPRD_ID: PRD_000262
• 分子名称: ENDOTHIAPEPSIN, 6-ammonio-N-{[(2R,3R)-3-{[N-(tert-butoxycarbonyl)-L-phenylalanyl-3-(1H-imidazol-3-ium-4-yl)-L-alanyl]amino}-4-cyclohexyl-2-hydroxybutyl](2-methylpropyl)carbamoyl}-L-norleucyl-L-phenylalanine (3 entities in total)
• 機能のキーワード: acid proteinase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Cryphonectria parasitica (chestnut blight fungus)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34762.06

構造登録者

Sali, A.,Veerapandian, B.,Cooper, J.B.,Foundling, S.I.,Hoover, D.J.,Blundell, T.L. (登録日: 1991-01-02, 公開日: 1991-04-15, 最終更新日: 2024-10-09)

主引用文献

Sali, A.,Veerapandian, B.,Cooper, J.B.,Foundling, S.I.,Hoover, D.J.,Blundell, T.L.
High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.
EMBO J., 8:2179-2188, 1989

PubMed Abstract: The conformation of the synthetic renin inhibitor CP-69,799, bound to the active site of the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6), has been determined by X-ray diffraction at 1.8 A resolution and refined to the crystallographic R factor of 16%. CP-69,799 is an oligopeptide transition--state analogue inhibitor that contains a new dipeptide isostere at the P1-P1' position. This dipeptide isostere is a nitrogen analogue of the well-explored hydroxyethylene dipeptide isostere, wherein the tetrahedral P1' C alpha atom has been replaced by trigonal nitrogen. The inhibitor binds in the extended conformation, filling S4 to S3' pockets, with hydroxyl group of the P1 residue positioned symmetrically between the two catalytic aspartates of the enzyme. Interactions between the inhibitor and the enzyme include 12 hydrogen bonds and extensive van der Waals contacts in all the pockets, except for S3'. The crystal structure reveals a bifurcated orientation of the P2 histidine side chain and an interesting relative rotation of the P3 phenyl ring to accommodate the cyclohexyl side chain at P1. The binding of the inhibitor to the enzyme, while producing no large distortions in the enzyme active site cleft, results in small but significant change in the relative orientation of the two endothiapepsin domains. This structural change may represent the action effected by the proteinase as it distorts its substrate towards the transition state for proteolytic cleavage.

PubMed: 2676515

実験手法

X-RAY DIFFRACTION (1.8 Å)