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Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133F from Thermus thermophilus
4GP4

Structural Similarities for the Entities in PDB 4GP4

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
Description: Cytochrome c oxidase subunit 1 protein
Length: 568
No structure alignment results are available for 4GP4.A explicitly.

It is represented by chain 3S8G.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 3S8G.A

 
 
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To see how chain 4GP4.A compares with the representative chain PDP:3S8GAa select a method below:





Entity #2: Chains: B
Description: Cytochrome c oxidase subunit 2 protein
Length: 168
No structure alignment results are available for 4GP4.B explicitly.

It is represented by chain 3S8G.B which is 100% sequence identical.

 Click here to show the structure comparison results for representative 3S8G.B

 
 
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To see how chain 4GP4.B compares with the representative chain PDP:3S8GBa select a method below:





Entity #3: Chains: C
Description: Cytochrome c oxidase polypeptide 2A protein
Length: 34
No structure alignment results are available for 4GP4.C explicitly.

It is represented by chain 3S8G.C which is 100% sequence identical.

 Click here to show the structure comparison results for representative 3S8G.C

 
 
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To see how chain 4GP4.C compares with the representative chain PDP:3S8GC_ select a method below:





  • Update Status Hide
    Aug 26 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.