Sandbox Reserved 960

This Sandbox is Reserved from 15/11/2014, through 15/05/2015 for use in the course "Biomolecule" taught by Bruno Kieffer at the Strasbourg University. This reservation includes 3fe9 through 3cdn.

To get started: Click the edit this page tab at the top. Save the page after each step, then edit it again. Click the 3D button (when editing, above the wikitext box) to insert Jmol. show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page. Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc. More help: Help:Editing

Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand at pH 5.5

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Updated on 22-December-2014 Function 7 helixes H1 H2 H3 H4 H5 H6 H7 Structure File:3fe6 cartoon.jpg Fig.1 Ribbon colored representation ASP1 is composed of 7 right-handed alpha helixes[ https://www.genome.jp/dbget-bin/www_bget?pdb:3FE6] H1: residues 8–25 H2: residues 27–36 H3: residues 42–56 H4: residues 66–74 H5: residues 75–77 H6: residues 78–90 H7: residues 96–112 H1 has a break in the hydrogen-bonding pattern of its structure, forming tight substitute hydrogen bonds with water molecules. Thus, it results in a kink (at residue Ala 14)(scene) induced by a disruption in the helical conformation, due to hydrogen bonds with water molecules. The C terminal(scene) domain of this molecule presents a characteristic PBP-GOP domain. While this protein is composed of 144 residues the domain PBP begin at 25 residue. ASP1 binds its ligand at low pH and releases it at neutral pH. Components implicated in the structure rigidity: ASP1 presents three disulfide bridges which are greatly enhancing its structure’s rigidity by linking four of the helixes together. The first disulfide bridge is established between H1 and H3 through Cysteins 20 and 51. An other disulfide bridge links H3 and H6 through Cys 47 and 98, and the third disulfide bridge connects H5 and H6 thanks to Cys 89 and Cys 107. Furthermore, non covalent bonds also play an important role. Indeed, at pH 5.5, Asp 66 and Leu 58 establish an hydrogene bond which is able to fix a key component structure such as H4. (scene) With their hydrogene bond Val 118 and Ile 119 stabilize alpha helix 2 and C terminal’s position. (scene) Cavity The dynamic structure of the protein is responsible of the ligand’s binding by adjustement of position. The structure looses its flexibility when CMJ binds. The successful delivery of the effector to the receptor relies on this property. The ligand accepting entry of the cavity is formed by H2, H4 and H5 (scene). However, the inside of the cavity is formed by the loop between helixes H3 and H4, and the region from H4 to H5(scene). The cavity is prone to accept such ligand because of its specific composition. Indeed, cavity components are mainly hydrophobic and aromatic and are localized in the same faces of the helix.Thus, it implies that this residues are regularly distant in the primary structure. Ligands Fig.2 CMJ Ligplot CMJ CMJ binding Fig.3 GOL Ligplot GOL Ligand GOL binding residues Fig.4 Cl Ligplot Cl Ligand Cl binding residue Disulfide bridges first disulfide bridge second disulfide bridge third disulfide bridge hydrophobic residues (A REFAIRE) acidic residues Related Forms Autres versions de la protéine à pH variable 3fe8 The same protein in complex with a serendipitous ligand soaked at pH 4.0 3fe9 The same protein in complex with a serendipitous ligand soaked at pH 7.0 3cdn The same protein in apo form soaked at pH 4.0 2h8v The same protein in apo form at pH 5.5 3cz2 The same protein in apo form at pH 7.0 3bfa The same protein in complex with the QMP at pH 5.5 3bfb The same protein in complex with the 9-ODA at pH 5.5 3bfh The same protein in complex with the HDOA at pH 5.5 3bjh The same protein in complex with the nBBSA at pH 5.5 3cyz The same protein in complex with the 9-ODA at pH 7.0 3cz0 The same protein in complex with the QMP at pH 7.0 3cz1 The same protein in complex with the nBBSA at pH 7.0 3cab The same protein in complex with the nBBSA soaked at pH 7.0 Structural highlights This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.