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Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle
4LD9

Structural Similarities for the Entities in PDB 4LD9

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,E
Description: Histone H3.2 protein
Length: 136
No structure alignment results are available for 4LD9.A, 4LD9.E explicitly.

These chains are represented by chain 1TZY.C which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1TZY.C

 
 
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Entity #2: Chains: B,F
Description: Histone H4 protein
Length: 103
No structure alignment results are available for 4LD9.B, 4LD9.F explicitly.

These chains are represented by chain 1TZY.D which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1TZY.D

 
 
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To see how chain 4LD9.F compares with the representative chain d1tzyd_ select a method below:





Entity #3: Chains: C,G
Description: Histone H2A protein
Length: 130
No structure alignment results are available for 4LD9.C, 4LD9.G explicitly.

These chains are represented by chain 4CAY.A which has more than 50% sequence identity.

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

 
 
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To see how chain 4LD9.G compares with the representative chain PDP:4CAYAa select a method below:





Entity #4: Chains: D,H
Description: Histone H2B 1.1 protein
Length: 126
No structure alignment results are available for 4LD9.D, 4LD9.H explicitly.

These chains are represented by chain 1TZY.B which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 1TZY.B

 
 
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Entity #5: Chains: I
Description: Widom 601 sequence reverse dna
Length: 167

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

 




Entity #6: Chains: J
Description: Widom 601 sequence forward dna
Length: 167

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

 




Entity #7: Chains: K,L
Description: Regulatory protein SIR3 protein
Length: 236
No structure alignment results are available for 4LD9.K, 4LD9.L explicitly.

These chains are represented by chain 4KUI.A which is 100% sequence identical.

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

 
 
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To see how chain 4LD9.L compares with the representative chain PDP:4KUIAa select a method below:





  • Update Status Hide
    Oct 21 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.