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X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin
4KMU

Structural Similarities for the Entities in PDB 4KMU

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,F,G
Description: DNA-directed RNA polymerase subunit alpha protein
Length: 329
No structure alignment results are available for 4KMU.A, 4KMU.B, 4KMU.F, 4KMU.G explicitly.

These chains are represented by chain 2A6H.A which has more than 40% sequence identity.

 Click here to show the structure comparison results for representative 2A6H.A

 
 
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To see how chain 4KMU.G compares with the representative chain d2a6ha1 select a method below:





Entity #2: Chains: C,H
Description: DNA-directed RNA polymerase subunit beta protein
Length: 1342
No structure alignment results are available for 4KMU.C, 4KMU.H explicitly.

These chains are represented by chain 4LK0.C which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4LK0.C

 
 
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To see how chain 4KMU.H compares with the representative chain PDP:4LK0Ca select a method below:





Entity #3: Chains: D,I
Description: DNA-directed RNA polymerase subunit beta' protein
Length: 1407
No structure alignment results are available for 4KMU.D, 4KMU.I explicitly.

These chains are represented by chain 4LK0.D which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4LK0.D

 
 
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To see how chain 4KMU.I compares with the representative chain PDP:4LK0Da select a method below:





Entity #4: Chains: E,J
Description: DNA-directed RNA polymerase subunit omega protein
Length: 91
No structure alignment results are available for 4KMU.E, 4KMU.J explicitly.

These chains are represented by chain 4LK0.E which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4LK0.E

 
 
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To see how chain 4KMU.J compares with the representative chain PDP:4LK0Ea select a method below:





Entity #5: Chains: X,Y
Description: RNA polymerase sigma factor RpoD protein
Length: 613
No structure alignment results are available for 4KMU.X, 4KMU.Y explicitly.

These chains are represented by chain 4LK1.F which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4LK1.F

 
 
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To see how chain 4KMU.Y compares with the representative chain PDP:4LK1Fa 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.

     
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Documentation

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