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CAPRI: Critical Assessment of PRediction of Interactions
 
  
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 MSD  CAPRI: Critical Assessment of PRediction of Interactions

Round 5 of CAPRI community wide experiment on the comparative evaluation of protein-protein docking for structure prediction

Hosted By EMBL/EBI-MSD Group

Targets

Please use these files for standard chain Identifiers
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.

Target 14: PROTEIN SERINE/THREONINE PHOSPHATASE-1 complex with MYOSIN PHOSPHATASE TARGETING SUBUNIT 1

From: Roberto Dominguez (Boston Biomedical Research Institute)


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  • CAPRI5-14 CLOSED 16-02-2004

    Structure Published see
    Structural basis of protein phosphatase 1 regulation
    MOHAMMED TERRAK, FREDERIC KERFF, KNUT LANGSETMO, TERENCE TAO & ROBERTO DOMINGUEZ
    Nature AOP, published online 26 May 2004
    For subscribers see Click here
    PDB entry 1S70 has been released
    COMPLEX BETWEEN PROTEIN SER/THR PHOSPHATASE-1 (DELTA) AND THE MYOSIN PHOSPHATASE TARGETING SUBUNIT 1 (MYPT1)


    Target 18: A. niger xylanase - TAXI

    From: Stefaan Sansen & Anja Rabijns (Leuven, Belgium)

    Target 18 is a complex between the TAXI xylanase inhibitor (bound) and A. niger xylanase (PDB entry 1UKR). TAXI is unrelated to XIP of Targets 16 and 17.

    Target 18 paper published


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  • CAPRI5-18


    Target 19: Ovine prion-FAB complex

    NOW PUBLISHED F.Eghiaian,J.Grosclaude,S.Lesceu,P.Debey,B.Doublet, E.Treguer,H.Rezaei,M.Knossow 2004, PNAS 101:10254.
    PDB entries 1TPX, (114-234) ovine recombinant prp ARQ variant
    1TQB ovine recombinant prp(127-228), VRQ variant
    1TQC ovine recombinant prp(127-228), ARR variant
    all in complex with the VRQ14 FAB fragment (IGG2A)


    From: M. Knossow LEBS-CNRS, Gif-sur-Yvette, France

    Target 19 Ovine prion-FAB complex. Unbound ovine prion to be model from PDB entry 1DWY an NMR set of coordinates of bovine prion (residues 121-230) The FAB coordinates are from the bound complex. The Ovine fragment consists of the residues and alignment

     
     1dwy_A -------------GLGGYMLGSAMSRPLIHFGSDYEDRYYRENMHRYPNQVYYRPVDQYS
    T19 HVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDRYS
    ******************.***********:************.**
    1dwy_A NQNNFVHDCVNITVKEHTVTTTTKGENFTETDIKMMERVVEQMCITQYQRESQAYYQ---
    T19 NQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGA
    ***************:******************:**********************
    1dwy_A -
    T19 S


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  • CAPRI5-19


    Target 15 Cancellation

    Dear CAPRI participants,

    We have to cancel Target 15 at the very last minute, because EMBO Journal was unexpectedly efficient in processing the paper by Graille et al., and some of you have seen it on the Web site of the journal. As the PDB will release the coordinates in coming days, those of you who had their predictions ready will be able to assess them.

    Sorry once again!

    The Management Committee

    Target 15 is now available in the PDB as PDB entrry 1v74

    Targets T16 and T17 Cancellation

    On behalf of the Management Committe, I'm sorry to inform you that Targets 16 and 17 have been cancelled. The Web page of the Gemini EU project on amylases http://www.ifr.bbsrc.ac.uk/Gemini/results.html displays a picture of the X-ray structures. We thank Michael Tress in Madrid for pointing that out. The picture has been on the Web since early January, making it impossible to guarantee that any prediction of T16 and 17 have been performed blindly. Thus, the Management Committee decided to cancel the two targets.

    Sorry about that, and our apologies to all of you who worked hard on predicting these targets. There are three more to do in the next two weeks. Good luck with those.


    Target 15: T15 ImmD-ColD

    From: Marc Graille and Herman van Tilbeurgh (Gif-sur-Yvette)

    Complex between the ImmD immunity protein and the catalytic domain of Colicin D (Marc Graille and Herman van Tilbeurgh, LEBS-CNRS, Gif-sur-Yvette, France). Both molecules are taken from the complex; surface side chains have been shaved to the C-beta, and the orientation is random.

    T15 PDB entry 1V74 has been released


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  • CAPRI5-15


    Target 16: A. nidulans xylanase - XIP

    From: Alain Roussel (AFMB, Marseille, France)

    Target 16 is a complex between the XIP-1 xylanase inhibitor (PDB entry 1OM0) and A. nidulans xylanase, which is highly similar to P. simplicissimum xylanase (PDB entry 1BG4), from which it can be homology-built.

    T16 PDB entry 1TA3 has been released

    Its sequence is: A. nidulans (xylanase famille 10)

    ASLNDLFVAAGKSYFGTCSDQALLQNSQNEAIVASQFGVITPENSMKWDALEPSQGNF
    GWSGADYLVDYATQHNKKVRGHTLVWHSQLPSWVSSIGDANTLRSVMTNHINEVVGRY
    KGKIMHWDVVNEIFNEDGTFRNSVFYNLLGEDFVRIAFETARAADPDAKLYINDYNLD
    SASYAKTQAMASYVKKWLAEGVPIDGIGSQAHYSSSHWSSTEAAGALSSLANTGVSEV
    AITELDIAGAASSDYLNLLNACLNEQKCVGITVWGVSDKDSWRASDSPLLFDGNYQPK
    DAYNAIVNALS


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  • CAPRI5-16


    Target 17: P. funiculosum xylanase - XIP

    From: Alain Roussel (AFMB, Marseille, France)

    Target 17 is a complex between the XIP-1 xylanase inhibitor (PDB entry 1OM0) and P. funiculosum xylanase, which is unrelated to the A. nidulans enzyme of Target 16. It is related to A.niger xylanase (PDB entry 1UKR), from which it can be homology-built.

    For T17 PDB entry 1TE1has been released.

    Its sequence is: P. funiculosum (xylanase famille 11)

    ITTSQTGTNNGYYYSFWTNGGGEVTYTNGDNGEYSVTWVDCGDFTSGKGWNPANAQTVTYS
    GEFNPSGNAYLAVYGWTTDPLVEYYILESYGTYNPSSGLTSLGQVTSDGGTYDIYSTQRVN
    QPSIEGTSTFNQYWSVRTEKRVGGTVTTANHFAAWKALGLEMGTYNYMIVSTEGYESSGSS
    TITVS


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  • CAPRI5-17