Primary Citation PubMed: 11257232
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Characterisation of the anti-apoptotic function of survivin-DeltaEx3 during TNFalpha-mediated cell death.
(2007) Br J Cancer 96
PubMed: 17505517 | PubMedCentral: PMC2359927 | DOI: 10.1038/sj.bjc.6603768
According to the published structure of the XIAP BIR2-caspase-3 complex (PDB ID: 1I3O ( Riedl et al , 2001 ), Figure 2A , lower panel), the topological contact between survivin-ΔEx3 and active... caspase-3 is predicted to be through the globular BIR domain of survivin-ΔEx3 with the edge, but not with the catalytic pocket of the enzyme caspase-3 ( Figure 2A , upper panel).
Publication Year: 2007
Prediction of metal ion-binding sites in proteins using the fragment transformation method.
(2012) PLoS One 7
PubMed: 22723976 | PubMedCentral: PMC3377655 | DOI: 10.1371/journal.pone.0039252
For Zn 2+ –binding proteins, a near perfect match was found for chain A of the inhibitor of apoptosis protein DIAP1 (PDB ID∶1JD5)  and the template from chain E of the bacu... oviral IAP repeat-containing protein 4, BIR 2 (PDB ID∶1I3O)  ( Fig. 13 ).
Template constructed from chain E of the baculoviral IAP repeat–containing protein 4 (PDB ID∶1I3O).
Publication Year: 2012
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits.
(2012) BMC Bioinformatics 13 Suppl 2
PubMed: 22536869 | PubMedCentral: PMC3377905 | DOI: 10.1186/1471-2105-13-S2-S6
Results Correct pairwise interactions in decoys Three protein complexes of different number of chains, 3 (PDB ID: 1A0R), 4 (1NNU), 6 (1I3O) were used in this study.
B , a 1I3O decoy (6 chains) with a global RMSD of 14.17 Å but yields a correct prediction of chains A, B, C, and D (RMSD: 2.22Å).
Photofrin binds to procaspase-3 and mediates photodynamic treatment-triggered methionine oxidation and inactivation of procaspase-3.
(2012) Cell Death Dis 3
PubMed: 22785533 | PubMedCentral: PMC3406584 | DOI: 10.1038/cddis.2012.85
Surprisingly, the modification ratio of the active site (Cys-163)-containing peptide did not change following PDT in both experiments, indicating that either the active site was not modified, or the m... dification was too minor to be detected by MS. Mapping the susceptible Met residues in the 3D structure of procaspase-3 (PDB code: 1I3O, a.a. 32–174 and 176–277) 33 shows that Met-39 and Met-44 cluster together at the surface of each monomer ( Figure 6 ).
Positions of the Met residues are denoted in the caspase-3 structure (PDB code: 1I3O 33 ).
The structure of XIAP BIR2: understanding the selectivity of the BIR domains.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 23999295 | PubMedCentral: PMC3760131 | DOI: 10.1107/S0907444913016284
The structure was solved by molecular replacement with MOLREP from CCP 4 (Winn et al. , 2011 ▶ ) using the BIR2 chain from PDB entry 1i3o , which is the structure of the BIR2–caspase-3... complex (Riedl et al. , 2001 ▶ ).
Figure 1 Overlay of the XIAP BIR2 crystal structure at 1.35 Å resolution (orange), the NMR structure (green; PDB entry 1c9q ; Sun et al. , 1999 ▶ ) and the caspase-3-bound form (light blue; PDB entry 1i3o ; Riedl et al. , 2001 ▶ ).
Publication Year: 2013
A conservation and biophysics guided stochastic approach to refining docked multimeric proteins.
(2013) BMC Struct Biol 13 Suppl 1
PubMed: 24565106 | PubMedCentral: PMC3952451 | DOI: 10.1186/1472-6807-13-S1-S7
In addition to these dimers, we produced multimeric input structures by running the Multi-LZerD multimeric docking program without refinement [ 11 ] for protein complexes with the following PDB IDs: 1... 3O , 1JYO , 1LOG , 1QGW , 1VCB , 1W88 , 1WWW , 2BBK , 2PRG and 6RLX .
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