

PFRMAT ABF1
TARGET T0011
AUTHOR 6792-8330-8583 D.Gerloff & F.Cohen, UCSF, gerloff@cgl.ucsf.edu
AUTHOR 9774-5781-2699 S.Benner, UF and ETH, benner@chem.ethz.ch
REMARK (collaboration between the two groups)
REMARK Secondary structure was predicted according to Benner & Gerloff and
REMARK later refined based on the hypothesis that the heat shock protein 90 fold
REMARK might have a similar active site arrangement as found in the paper on
REMARK the ATPase domain of DNA gyrase B (found by SCOP browsing).
REMARK We are grateful to D.B. Wigley for forwarding us the gyrase coordinates
REMARK which were not available in the PDB. Upon closer comparison of our
REMARK secondary structure prediction and the conservation and biochemically
REMARK expected geometry of funtional residues around the active site with the
REMARK gyrase B structure, we reached the conclusion that this might present a
REMARK case of hidden homology and that the proteins were likely to adopt the
REMARK same topology exept for an inserted hairpin structure (54-70), and possible
REMARK differences in the region (86-117) which forms a lid in the gyrase structure
REMARK where the correspondence seemed to break down. Of course, the N- and
REMARK Our prediction is described in more detail in a manuscript submitted to Proteins
REMARK (prior to the deadline). Whereas the model might not be perfect, it fits very
REMARK remarkably well the prediction of the relative orientation of the secondary
REMARK structural elements towards a putative active site.
REMARK As always, the 3D model is submitted as a means for verification of the 2.1
REMARK prediction code (in a separate entry, SYBYL (Tripos) model). Due to time
REMARK constraints the model is likely to lack some of the loops, we apologize! Further,
REMARK we have not modelled the lid segment 86-117, although it should be possible
REMARK using a speculative autophosphorylation site serine as an anchor in a (true) ab
REMARK initio exercise. The location of the inserted hairpin structure is one of several
REMARK possibilities, probably our favorite...
BEGDAT 1.1  1  1.00
SS 220
M C  1.00
A C  1.00
S C  1.00
E C  1.00
T C  0.70
F E  0.70
E E  0.70
F E  0.70
Q E  0.70
A E  0.70
E E  0.60
I E  0.50
T C  0.80
Q H  0.70
L H  0.80
M H  0.80
S H  1.00
L H  1.00
I H  1.00
I H  1.00
N H  1.00
T H  1.00
V H  1.00
Y H  1.00
S H  0.80
N C  1.00
K C  1.00
E H  0.70
I H  1.00
F H  1.00
L H  1.00
R H  1.00
E H  1.00
L H  1.00
I H  1.00
S H  1.00
N H  1.00
A H  1.00
S H  1.00
D H  0.70
A H  0.70
L H  0.70
D C  0.70
K C  1.00
I E  0.70
R E  1.00
Y E  1.00
K E  1.00
S E  1.00
L E  1.00
S E  0.90
D C  0.90
P C  1.00
K C  1.00
Q C  0.80
L E  0.70
E E  0.70
T E  0.70
E E  0.60
P C  1.00
D C  0.90
L E  1.00
F E  1.00
I E  1.00
R E  1.00
I E  1.00
T E  0.90
P C  1.00
K C  1.00
P C  1.00
E C  1.00
Q C  1.00
K C  0.70
V E  1.00
L E  1.00
E E  1.00
I E  1.00
R E  1.00
D E  0.90
S E  0.70
G C  0.80
I C  0.80
G C  0.70
M C  0.70
T C  0.70
K C  0.90
A H  0.80
E H  0.90
L H  0.90
I H  0.90
N H  0.90
N H  0.90
L H  0.50
G C  0.50
T C  0.50
I C  0.50
A C  0.50
K C  0.80
S C  1.00
G C  1.00
T H  0.70
K H  0.80
A H  0.80
F H  0.80
M H  0.80
E H  0.50
A H  0.70
L H  0.70
S H  0.70
A C  0.90
G C  0.90
A C  0.90
D C  0.90
V C  0.70
S C  0.70
M C  0.60
I C  0.60
G C  0.60
Q C  0.60
F C  0.60
G C  0.60
V C  0.60
G H  0.50
F H  0.60
Y H  0.60
S H  0.60
L H  0.60
F H  0.60
L H  0.60
V H  0.50
A C  0.80
D C  1.00
R E  0.90
V E  1.00
Q E  1.00
V E  1.00
I E  1.00
S E  1.00
K C  0.80
S C  1.00
N C  1.00
D C  1.00
D C  0.80
E E  1.00
Q E  1.00
Y E  1.00
I E  1.00
W E  1.00
E E  0.80
S C  1.00
N C  1.00
A C  1.00
G C  1.00
G C  1.00
S C  0.90
F E  0.80
T E  0.80
V E  0.80
T E  0.80
L E  0.80
D E  0.60
E C  0.90
V C  1.00
N C  1.00
E C  1.00
R C  1.00
I C  0.90
G C  0.90
R C  0.80
G E  0.60
T E  1.00
I E  1.00
L E  1.00
R E  1.00
L E  1.00
F E  1.00
L E  0.70
K C  0.90
D C  1.00
D C  1.00
Q C  0.80
L C  0.80
E C  0.90
Y H  0.70
L H  0.70
E H  0.70
E H  0.70
K H  1.00
R H  1.00
I H  1.00
K H  1.00
E H  1.00
V H  1.00
I H  1.00
K H  1.00
R H  1.00
H H  1.00
S H  1.00
E H  1.00
F H  1.00
V H  1.00
A C  0.70
Y C  0.90
P C  1.00
I E  1.00
Q E  1.00
L E  1.00
V E  1.00
V E  0.90
T E  0.70
K C  1.00
E C  1.00
V C  0.70
E E  0.60
K E  0.60
E E  0.60
V E  0.60
P C  0.90
I C  0.90
P C  1.00
ENDDAT 1.1
BEGDAT 2.1  1  1.00 1
63
  1   2  --  0.00   0   0  0.00
  1   3  --  0.00   0   0  0.00
  1   4  --  0.00   0   0  0.00
  1   5  --  0.00   0   0  0.00
  1   6  --  0.00   0   0  0.00
  1   7  --  0.00   0   0  0.00
  1   8  --  0.00   0   0  0.00
  1   9  --  0.00   0   0  0.00
  1  10  --  0.00   0   0  0.00
  1  11  --  0.00   0   0  0.00
  1  12  --  0.00   0   0  0.00
  1  13  --  0.00   0   0  0.00
  1  14  --  0.00   0   0  0.00
  1  15  --  0.00   0   0  0.00
  1  16  --  0.00   0   0  0.00
  1  17  --  0.00   0   0  0.00
  2   6  PD  0.40   0   0  0.00
  2   8  --  0.00   0   0  0.00
  2   9  --  0.00   0   0  0.00
  2  10  PE  0.80   0   0  0.00
  3   4  OS  0.80   0   0  0.00
  3   7  PD  1.00   0   0  0.00
  3   8  --  0.00   0   0  0.00
  3   9  --  0.00   0   0  0.00
  3  10  OS  1.00   0   0  0.00
  3  14  OS  1.00   0   0  0.00
  3  15  PE  0.80   0   0  0.00
  4   7  HH  1.00   0   0  0.00
  4   8  --  0.00   0   0  0.00
  4   9  --  0.00   0   0  0.00
  4  16  KK  1.00   0   0  0.00
  5   6  HH  1.00   0   0  0.00
  5   8  --  0.00   0   0  0.00
  5   9  --  0.00   0   0  0.00
  6   8  --  0.00   0   0  0.00
  6   9  --  0.00   0   0  0.00
  7   8  --  0.00   0   0  0.00
  7   9  --  0.00   0   0  0.00
  7  14  HH  1.00   0   0  0.00
  8   9  --  0.00   0   0  0.00
  8  10  --  0.00   0   0  0.00
  8  11  --  0.00   0   0  0.00
  8  12  --  0.00   0   0  0.00
  8  13  --  0.00   0   0  0.00
  8  14  --  0.00   0   0  0.00
  8  15  --  0.00   0   0  0.00
  8  16  --  0.00   0   0  0.00
  8  17  --  0.00   0   0  0.00
  9  10  --  0.00   0   0  0.00
  9  11  --  0.00   0   0  0.00
  9  12  --  0.00   0   0  0.00
  9  13  --  0.00   0   0  0.00
  9  14  --  0.00   0   0  0.00
  9  15  --  0.00   0   0  0.00
  9  16  --  0.00   0   0  0.00
  9  17  --  0.00   0   0  0.00
 10  14  PD  0.70   0   0  0.00
 11  12  HH  1.00   0   0  0.00
 11  14  HH  1.00   0   0  0.00
 12  13  HH  1.00   0   0  0.00
 15  16  OS  1.00   0   0  0.00
 15  17  PD  1.00   0   0  0.00
 16  17  HH  1.00   0   0  0.00
ENDDAT 2.1
END

*******************************************************************************
Dietlind L. Gerloff                              * * *    Tel. (415) 502-5650
University of California San Francisco         * _   _ *  FAX  (415) 476-6515
Dept. of Cellular and Molecular Pharmacology  *  o   o  *
513 Parnassus ave                             *    .    *
SAN FRANCISCO, CA 94143-0450                   * \___/ *  email:
U.S.A.                                           * * *    gerloff@cgl.ucsf.edu
*******************************************************************************

