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Crystal structure of p19 complexed with 19-bp small interfering RNA
1R9F

Structural Similarities for the Entities in PDB 1R9F

The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2]. To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

Entity #1: Chains: B
Description: 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3' rna
Length: 21

This entity is not a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.

 



Entity #2: Chains: C
Description: 5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3' rna
Length: 21

This entity is not a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.

 



Entity #3: Chains: A
Description: Core protein P19 protein
Length: 136
No structure alignment results are available for 1R9F.A explicitly.

It is represented by chain 4J39.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4J39.A

 
 
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To see how chain 1R9F.A compares with the representative chain PDP:4J39Aa select a method below:




  • Update Status Hide
    Jan 27 2015

    Cluster data are up-to-date as of:
     
  • Table Legend Hide
    • Rank: current row position. Changes with different sorting orders and filter rules
    • Domain 2: Domain name of 2nd domain. Can be either a SCOP ID (d<PDB ID><Chain ID><Domain ID>), ProteinDomainParser ID (PDP:<PDB ID><Chain ID><Domain ID>)
    • Title: Protein chain description
    • P-value: P-value of this alignment (FATCAT) (default sorted by this)
    • Score: Raw alignment score (FATCAT)
    • RMSD: RMSD value of the alignment
    • Len1: Domain 1 length
    • Len2: Domain 2 length
    • %ID: % sequence identity in the alignment. A 40% sequence identity filter is applied before the structure alignments are calculated, so most results show low similarity. If the sequences are of vastly different lengths, the clustering procedure will group them in different clusters, even if they share a region of high sequence similarity.
    • %Cov1: The coverage, or %, of aligned residues in chain 1
    • %Cov2: The coverage, or %, of aligned residues in chain 2

    The table is sorting is by P-value by default. Clicking on the column header will change the sort order. Select the Filter Results lense img icon to apply other filtering criteria.

     
Comparison Tool

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PDB 1: Chain 1: ...
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Documentation

A detailed description of the procedure for the all vs. all alignments is available.