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Figure 3
Conformation-independent structural comparison in the presence of domain swaps. Models of barnase with different biological assemblies are compared; the model 1yvs chain A corresponds to the trimeric domain-swapped form, unlike the sequence-identical model 2za4 chain A. To help illustrate the nature of the conformational change, in (a) the N-terminus is labelled N and the N-terminal helix is labelled H1. The models are coloured by (a) the Flexible score and (b) the side-chain r.m.s.d. score using a colour gradient (yellow implies similarity and red relative dissimilarity; white, not applicable). This demonstrates the ability to analyse structural conservation despite the presence of large conformational changes such as domain swaps, noting that this approach does not require spatial relationships to be conserved nor domains to be intact; only the conservation of local structure is of relevance. (a) Flexible score: 1yvs chain A (top) and 2za4 chain A (bottom). (b) Side-chain r.m.s.d. score: 1yvs chain A (top) and 2za4 chain A (bottom).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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