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40-residue beta-amyloid fibril derived from Alzheimer's disease brain
2M4J

Structural Similarities for the Entities in PDB 2M4J

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: A,B,C,D,E,F,G,H,I
Description: Amyloid beta A4 protein protein
Length: 40
No structure alignment results are available for 2M4J.A, 2M4J.B, 2M4J.C, 2M4J.D, 2M4J.E, 2M4J.F, 2M4J.G, 2M4J.H, 2M4J.I explicitly.

These chains are represented by chain 3IFN.P which is 100% sequence identical.

 Click here to show the structure comparison results for representative 3IFN.P

 
 
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To see how chain 2M4J.I compares with the representative chain PDP:3IFNP_ select a method below:





  • Update Status Hide
    Dec 16 2014

    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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Documentation

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