21 August 1998  Christian

Here are the interesting alignments for t53-first:

1aqe/t53-first-1aqe-vit.pw.dist:1aqe              110        -5.77       -6.58
1ash/t53-first-1ash-global.pw.dist:1ash           147        -9.36       -9.62
1ash/t53-first-1ash-post.pw.dist:1ash             147        -9.36       -9.62
1ash/t53-first-1ash-vit.pw.dist:1ash              147        -5.78       -5.94
1atb/1atb-t53-first-fssp-global.pw.dist:T0053      60        -6.44       -6.39
1atb/t53-first-1atb-vit.pw.dist:1atb               62        -5.38       -5.28
1ctl/t53-first-1ctl-global.pw.dist:1ctl            85       -10.68      -10.21
1ctl/t53-first-1ctl-post.pw.dist:1ctl              85       -10.68      -10.21
1ctl/t53-first-1ctl-vit.pw.dist:1ctl               85        -7.88       -7.37
1erd/1erd-t53-first-fssp-global.pw.dist:T0053      60        -7.87       -5.79
1erd/1erd-t53-first-global.pw.dist:T0053           60        -7.04       -5.45
1erd/1erd-t53-first-post.pw.dist:T0053             60        -7.04       -5.45
1erd/1erd-t53-first-vit.pw.dist:T0053              60        -7.00       -6.28
1erd/t53-first-1erd-global.pw.dist:1erd            40        -6.44       -7.51
1erd/t53-first-1erd-post.pw.dist:1erd              40        -6.44       -7.51
1erd/t53-first-1erd-vit.pw.dist:1erd               40        -7.61       -6.51
1iml/t53-first-1iml-global.pw.dist:1iml            76        -9.29       -9.12
1iml/t53-first-1iml-post.pw.dist:1iml              76        -9.29       -9.12
1iml/t53-first-1iml-vit.pw.dist:1iml               76        -7.88       -7.73
1qli/t53-first-1qli-global.pw.dist:1qli            59        -7.97       -8.30
1qli/t53-first-1qli-post.pw.dist:1qli              59        -7.97       -8.30
1qli/t53-first-1qli-vit.pw.dist:1qli               59        -6.29       -5.42
1rlr/t53-first-1rlr-global.pw.dist:1rlr           737        -8.48       -6.48
1rlr/t53-first-1rlr-post.pw.dist:1rlr             737        -8.48       -6.48

The three structure 1ctl, 1iml, and 1qli are essentially the same
structure --- a metal-binding protein.  I favor the automatic
t53-first-1ctl-global and t53-first-1qli.cbarrett1.a2m alignments.
Tacked onto the t53/1fvkA/1fvkA-t53.cbarrett1.a2m alignment, it looks
like it would form a nice metal binding pocket.

t53-first-1ash-post.pw presents an interesting alternative to the
metal binding proteins.  Based on PMID:9150215, I interpreted it to
imply that t53 shouldhave an NAD+ binding site.  I don't know if NAD+
looks anything like an heme group, as is in 1ash. I will investigate.


1erd/t53-first-1erd-global
1erd/1erd-t53-first-vit
The 1erd alignments match a 17-residue short-helix/turn/short-helix piece of 
structure. The alignments are interesting because they conserve the turn and the
end of each helix where they meet up. It overlaps the beginning of the 1ash 
alignment.  If we want to get picky, it could be used to replace 
(and slightly extend) the beginning of the 1ash alignment.

1aqe/t53-first-1aqe-vit
The match for this alignment is mainly to a piece of helix.  For 1hvkA, we have already 
matched this region to helix.  A little hand fiddling, though, does result in an alignment
with lots of identity (t53-first-1aqe.cbarrett1.a2m).  It's not too promising, as the
rest of the match is to coil.

1rlr/t53-first-1rlr-global
just a fragment match to some helix.  Fiddling does not result in an alignment to compact
structure.

1atb/1atb-t53-first-fssp-global
fragment match to some coil.  Fiddling does nothing convincing.