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Distance spread is larger in 2K39 than in 6V5D for 163 of 167 tested 1UBQ contacts.

For 167 C-alpha residue pairs selected by a fixed 1UBQ crystal reference, the 2K39 ubiquitin ensemble had larger population distance SD than the 6V5D ensemble for 163 pairs. The median pairwise SD ratio was 1.7200498882688864, while their majority contact graphs shared 164 of 172 contacts (Jaccard index 0.9534883720930233). This comparison uses archived PDB revisions and equal weights for deposited models; it measures coordinate spread, not motion in solution or ensemble quality. Model construction, shared source information, coordinate uncertainty, and pair dependence limit interpretation. No hypothesis test, biological confidence interval, or held-out solution test was performed.

ubiquitin · protein structure · distance spread · contact graph · NMR ensemble · C-alpha distance

Admitted 1 citing publication

References

11
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    [Legacy relation: reproduces] Used its eight checksum-verified PDB coordinate and metadata snapshots. New Kabsch code reproduced its 12 correlation rows and all 24 coefficients with maximum absolute error 0 in this environment.

  2. Deposited-model and cutoff sensitivity of ubiquitin Cα contact maps sci:sha256:48903fcc23599e9ca1df58d55fee49705b5ce8c4dd81ebe1cf50a5d6abb4ea7d

    [Legacy relation: reproduces] New distance code reproduced the primary majority, union, invariant, and variable contact counts for four entries. It also reproduced the 2K39 versus 6V5D graph intersection of 164 and union of 172. This comparison motivated the fixed-contact distance-spread question.

  3. usesdoi:10.2210/pdb1ubq%2Fpdb

    The 1UBQ archived structure was used as the fixed reference to select the 167 primary residue pairs.

  4. usesdoi:10.2210/pdb1d3z%2Fpdb

    The 1D3Z archived structure was included in context analyses and prior-table checks.

  5. usesdoi:10.2210/pdb2k39%2Fpdb

    The 2K39 archived structure ensemble was used in the primary distance-spread comparison.

  6. usesdoi:10.2210/pdb6v5d%2Fpdb

    The 6V5D archived structure ensemble was used in the primary distance-spread comparison.

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  10. supportsdoi:10.1371/journal.pcbi.0040043

    This paper discusses limits of structural alignment; that context supports computing within-model distances without structural alignment.

  11. doi:10.2174/138920310794109201

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