The files 1bcc.pdb and 3bcc.pdb in this directory are the coordinate files submitted to the Brookhaven Protein Database in March 98 as updates for entries 1bcc and 3bcc.

This file contains the coordinates for the complete dimer of the native complex.

This file contains the coordinates for the complete dimer of the complex containing stigmatellin and antimycin.

This file contains the coordinates for the three catalytic subunits of the "functional monomer" of the native complex, abstracted from the file 1bccdimref.pdb.

This file contains the coordinates for the three catalytic subunits of the "functional monomer" of the complex containing stigmatellin and antimycin, abstracted from the file 3bccdimref.pdb.

This file contains the coordinates for the three catalytic subunits of the "functional monomer" of the complex from the file 1bcc_m.pdb. The coordinates for the ISP from 3bcc_m.pdb, p65.pdb, and p6522.pdb (the latter two from the Iwata et al structures, rotated to the same reference coordinate system) have been added, so that coordinates for the ISP in four positions are in the same file. The quinone at the Q_i-site has been retained, phospholipid and detergent molecules have been removed, and two quinone molecules added at the Q_o-site. These have been positioned in the structure as follows:

1. The quinone from file 4rcr.pdb (reaction center of Rb. sphaeroides) was positioned in the distal lobe of the Q_o-site so as to bring the -C=O of the quinone ring within H-bond distance of Ne of His-161 of ISP (this mimicks the interaction with stigmatellin). The structure was then relaxed through energy minimization using SCULPT.

2. The quinone was removed, and another copy positioned with the quinone head group in the proximal lobe, in the position occupied by the pharmacophore of myxothiazol. This structure was then relaxed using SCULPT. The energy minimization ensured that there was no overlap of atoms of either quinone separately with the protein.

3. The coordinates of the quinone in the distal lobe were then added back to the files, so that a set for both quinones was present.

4. The coordinates for Glu-272 from 1bcc were deleted, and replaced by two sets, the coordinates from 2bcc (to show the suggested ligation of quinol by this side chain), or from the myxothiazol containing structure (to show the position when the proximal lobe of the Q_o-site is occupied). These structures were added as separate heterogroups, and a H-atom was added to simulate either H of the quinol -OH in the H-bond with Glu-272, or of the Glu-272 -COOH in the two different positions.

5. The water chain in the channel from the P-side aqueous phase into cyt b to reach the Q_o-site and the heme b_L propionate was taken from a model generated for a steered molecular dynamics simulation of the ISP movement (Izrailev, S., Crofts, A.R., Berry, E.A. and Schulten. K. (1999) Biophys. J. 77, 1753-1768). The water nearest the quinone was relaxed to make room for the Glu-272 side chain.

"Electrons" were added to the file by positioning 4 H-atoms along the vector connecting redox centers involved in the different partial reactions, and "H-atoms" added to the quinone carbonyl of Q_{o, distal}, and the Ne of His-161.

The Chime animation works by redrawing the structure in each frame, with different elements turned on or off.