POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

The Crystal structure of PDE6D in complex with the inhibitor (s)-5
4JVF

Structural Similarities for the Entities in PDB 4JVF

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: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta protein
Length: 152
No structure alignment results are available for 4JVF.B explicitly.

It is represented by chain 4JV8.B which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4JV8.B

 
 
  Loading...

To see how chain 4JVF.B compares with the representative chain PDP:4JV8Ba select a method below:





  • Update Status Hide
    Nov 18 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

Calculate pairwise sequence or structure alignments.

PDB 1: Chain 1: ...
PDB 2: Chain 2: ...
Align custom files (Launches a Java Web Start application)
 

Documentation

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