POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

NEMO CC2-LZ DOMAIN - 1D5 DARPIN COMPLEX
2V4H

Structural Similarities for the Entities in PDB 2V4H

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
Description: NF-KAPPA-B ESSENTIAL MODULATOR protein
Length: 110
No structure alignment results are available for 2V4H.A, 2V4H.B explicitly.

These chains are represented by chain 4BWN.A which has more than 90% sequence identity.

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

 
 
  Loading...

To see how chain 2V4H.B compares with the representative chain PDP:4BWNAa select a method below:





Entity #2: Chains: C,D
Description: 1D5 DARPIN protein
Length: 136
No structure alignment results are available for 2V4H.C, 2V4H.D explicitly.

These chains are represented by chain 4DUI.A which has more than 70% sequence identity.

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

 
 
  Loading...

To see how chain 2V4H.D compares with the representative chain PDP:4DUIAa select a method below:





  • Update Status Hide
    Dec 02 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.