Critical Assessment of PRediction of Interactions
Third community wide experiment on the comparative
evaluation of protein-protein docking for structure
Hosted By EMBL/EBI-MSD Group
Please use these files for standard
PLEASE NOTE: For submissions only files uploaded that conform
to the format defined in the starting files and described
in the format document will be
accepted as valid submissions. The submission procedure will
automatically reject files that fail format checking.
Targets 08: Nidogen-G3/laminin (unbound/bound)
T08 is from Pr. Timothy A. Springer (Harvard Medical School) CAPRI3-08 Nidogen-G3/laminin EGF
Nidogen-G3 domain (bound) in complex with three laminin EGF-like modules
1KLO (Stetefeld et al., 1996, JMB 257:644)
Nidogen-G3 is known to bind mostly, but not necessarily exclusively,
to the middle domain (residues 65-120) of the laminin fragment.
We suggest docking nidogen-G3 on the whole fragment and on the
middle domain separately. However, only ten solutions will be
permitted in total.
NOTE: For target 08 there has been a query about what to submit
- does one submit coordinates for all three domains of laminin docked
to nidogen or just he middle domain? The management committee has
after consulting with Shoshana, decided on the simplest path, i.e.
models obtained by docking on one laminin modules will contain only
that module; models obtained by docking on three modules will contain
all three. They should still be ranked and go into a single file.
During the assessment procedure this will be taken into account in a
manner as yet to be decided.
Target T09: Wild type LicT homodimer (unbound/unbound)
Target 9 Published: see:
J Biol Chem. 2005 Feb 7; [Epub ahead of print]
Activation of the LicT transcriptional antiterminator involves a domain
swing/lock mechanism provoking massive structural changes.
Graille M, Zhou CZ, Receveur-Brechot V, Colinet B, Declerck N, van
T09 is from Pr. Herman van Tilbeurgh (Orsay) CAPRI3-09 wild type LicT homodimer
Aim: Reconstruct the wild type LicT homodimer
The structure of the H207D/H269D mutant has been published
(van Tilbeurgh et al., 2001, EMBO J 20:3789)
but it forms a different dimer. Use the 1H99 file after
mutating Asp207 and Asp269 back to His. Ten (ranked) solutions
can be submitted.
T09 is wild-type LicT, with the same two domains as in 1H99
and no phosphorylation.