Index of /cytbc1/PDB
Name Last modified Size Description
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Parent Directory 31-Jan-2013 21:57 -
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vsclmwred.pdb 16-Aug-2006 01:11 223k
uq6.pdb 16-May-2001 14:30 3k
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tmp/ 05-Jul-2006 20:17 -
![[TXT]](/icons/text.gif)
stgnatdif2.tbl 14-Feb-1998 17:01 6k
stgnatdif.tbl 14-Feb-1998 17:01 6k
sqr401coord.pdb 25-Apr-2012 12:10 1.4M
rcsb031797.pdb-update 02-Mar-2005 21:49 827k
rbcp2i.pdb 26-Feb-2007 12:23 1021k
rbciref.pdb 26-Feb-2007 12:23 1021k
rbcapsbc1.pdb 27-Sep-2004 14:25 1010k
rbc343.pdb 08-Feb-2007 15:53 1021k
pdb1ppj.ent 08-May-2006 17:46 2.8M
p84dimref.pdb 06-Aug-2003 16:16 2.5M
old/ 29-Jun-2004 01:15 -
ntzdimref.pdb 24-Mar-2005 17:59 2.6M
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makedir.csh 19-Jan-2000 10:23 1k
l0ndimref.pdb 10-Apr-2003 00:50 2.6M
l0ldimref.pdb 11-Apr-2003 01:43 2.6M
kyodimref2.pdb 05-Mar-2002 18:07 2.8M
kb9dimref.pdb 17-Sep-2002 22:04 2.5M
iwp65ref.pdb 07-Oct-1998 11:37 2.3M
iwp6522ref.pdb 07-Oct-1998 11:37 2.4M
index.html.0 20-Jan-2000 00:05 2k
ezvdimref.pdb 25-Jun-2001 14:20 2.5M
cbczn3.pdb 18-Jan-2006 11:26 2.4M
bczn3ref.pdb 21-Feb-2000 16:32 2.5M
bcstgref.pdb 26-Jan-1999 09:57 2.4M
bcnatref.pdb 26-Jan-1999 09:56 2.4M
bcmyxref.pdb 28-Jun-2004 23:09 2.5M
bcmoaref.pdb 29-Jun-2004 01:16 2.5M
bchexdimref.pdb 28-May-1999 12:11 2.4M
bcchgref.pdb 26-Jan-1999 09:54 2.4M
bbcy21ref.pdb 22-Sep-2004 10:47 2.6M
NU1dimrefc.pdb 24-Feb-2005 13:45 2.6M
NU1dimref.pdb 24-Mar-2005 17:57 2.6M
3bccref.pdb 28-May-1999 12:34 2.3M
3bcc.pdb 09-Dec-1998 09:20 2.3M
2ppjref.pdb 24-Mar-2005 18:06 2.6M
2bccref.pdb 29-Mar-2000 11:52 2.4M
2FBW-update.pdb 10-Jan-2006 23:08 1.5M
1zrtref.pdb 03-Jul-2006 12:47 1.0M
1yq3.pdb 11-Mar-2005 19:31 1k
1sqxdimref.pdb 25-Sep-2005 14:27 2.5M
1sqvdimref.pdb 25-Sep-2005 14:38 2.5M
1qcrref.pdb 16-Oct-1998 00:57 187k
1qcrdimref.pdb 16-Oct-1998 13:57 333k
1ppjref.pdb 23-Feb-2005 12:09 2.6M
1ppj.pdb 08-Jul-2004 11:18 2.8M
1pp9ref.pdb 22-Sep-2004 10:51 2.6M
1pp9.pdb 08-Jul-2004 11:18 1.4M
1nek3mer.pdb 11-Apr-2003 12:15 2.0M
1bccref.pdb 28-May-1999 12:34 2.4M
1bcc3bcc.not 17-Feb-2003 13:14 4k
1bcc.pdb 09-Dec-1998 09:21 2.3M
This directory contains coordinates files (.pdb) specially prepared
to facilitate comparing different structures and looking at protein
interactions in the dimer which are not present in the monomer.
While some of the structures are our own unpublished work, we have
also taken files from the PDB.
The coordinates were manipulated as follows:
1. Dimerization- where only a monomer was submitted to the PDB, we
have generated the dimer using crystallographic or non-crystallo
graphic symmetry, as appropriate.
2. Superposition- The structures have been rotated and translated
to bring them ito a standard reference position in which the dimer
2-fold axis is along the Z axis, with the N-side toward positive Z.
Since the structures are all superposed, they can be compared
directly if one's viewer allows loading two molecules, or the same
figure can be made from each structure using the same orientation.
In this position we estimate that the P-surface of the bilayer
hydrophobic zone is at about z=28, and the N surface at z=68.
Thus a rough estimate of the fractional way across the dielectric
for any given atom at (x,y,z) is given by (z-28)/40
3. Chains have been lettered according to the scheme in use here,
with subunits 1-11 labeled A-K in one monomer and N-X in the second.
Acknowledgement and disclaimer- The coordiantes for structures
solved in other labs were taken from the database and manipulated
as described above. All credit for the structures belongs to the
depositors, and we take responsibility for any errors introduced.
However our responsibility is limited to our sincere apologies
and a promise to promptly correct any errors that are brought to
our attention.
We make no warranty of the suitability of these files for any
purpose.
The files 1bcc.pdb and 3bcc.pdb in this directory are the coordinate files
obtained, after further refinement and error correction, from the same
datasets used for the structures 1BCC and 3BCC submitted to the
Brookhave Protein Database in March 98.
------------------------------------------------
1bcc is the structure of the chicken cytochrome bc1 complex from a native
crystal. Ubiquinone at the Qi site, two PE molecules, and one OG, are
modeled as residues 5, 6, 7, and 8 in chain L. One monomer is presented,
the NCS-related monomer can be generated by applying a transform which
can be expressed in O datablock form as:
.lsq_rt_ncs1bcc r 12 (3f14.7)
-0.8350813 -0.5501187 -0.0026849
-0.5501213 0.8350376 0.0089561
-0.0026850 0.0089561 -0.9999563
129.0778355 37.8589104 171.4586645
The structure is presented at its coordinates in its native unit cell.
To transform to a reference cell with the dimer 2-fold along the z axis,
apply the inverse of the transform (ODB formnat):
.lsq_rt_ref21bcc R 12 (3f15.6)
0.018675 0.010478 -0.999771
0.957703 0.287004 0.020898
0.287158 -0.957872 -0.004675
17.905149 174.485565 86.488541
------------------------------------------------
3bcc is the structure from a crystal containing stigmatellin and antimycin.
Models for these inhibitors are present as residues 5 and 6 of chain L.
One monomer is presented, the NCS-related monomer can be generated by
applying a transform which can be expressed in O datablock form as:
.lsq_rt_ncs3bcc r 12 (3f14.7)
-0.8230250 -0.5680065 -0.0002017
-0.5680039 0.8230247 0.0006473
-0.0002021 0.0006488 -0.9999998
129.9098500 40.4159859 170.0044933
The structure is presented at its coordinates in its actual unit cell.
To transform to a reference cell with the dimer 2-fold along the z axis,
apply the inverse of the transform (ODB formnat):
.lsq_rt_ref23bcc R 12 (3f15.6)
0.005187 0.001972 -0.999984
0.954718 0.297463 0.005539
0.297468 -0.954732 -0.000339
17.472937 172.602783 85.056358
------------------------------------------------
The format of the "O" datablock rotation-translation operators
given here is as follows:
Lines 2-5 contain the transpose of the rotation matrix
Line 6 contains a translation vector to be applied after the rotation.
This operator can be used by CCP4 PDBSET program with the syntax:
transform [invert] ODB filename.o
1bccref.pdb and 3bccref.pdb are dimers of the same structure,
moved to a reference cell in which they should be superimposable.
The dimer 2-fold is along the Z axis in this reference cell.