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Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
4FYD

Structural Similarities for the Entities in PDB 4FYD

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: DNA polymerase alpha catalytic subunit A protein
Length: 910
No structure alignment results are available for 4FYD.A, 4FYD.B explicitly.

These chains are represented by chain 4FVM.A which has more than 95% sequence identity.

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

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




Entity #2: Chains: C,D
Description: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3') dna
Length: 25

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

 



Entity #3: Chains: E,F
Description: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3') hybrid
Length: 12

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

 



  • Update Status Hide
    Jan 27 2015

    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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PDB 1: Chain 1: ...
PDB 2: Chain 2: ...
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Documentation

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