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12-subunit RNA Polymerase II
2B8K

Structural Similarities for the Entities in PDB 2B8K

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
Description: DNA-directed RNA polymerase II largest subunit protein
Length: 1733
No structure alignment results are available for 2B8K.A explicitly.

It is represented by chain 1TWF.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1TWF.A

 
 
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To see how chain 2B8K.A compares with the representative chain d1twfa_ select a method below:





Entity #10: Chains: J
Description: DNA-directed RNA polymerases I/II/III subunit 10 protein
Length: 70
No structure alignment results are available for 2B8K.J explicitly.

It is represented by chain 4C2M.J which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4C2M.J

 
 
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To see how chain 2B8K.J compares with the representative chain PDP:4C2MJa select a method below:





Entity #11: Chains: K
Description: DNA-directed RNA polymerase II 13.6 kDa polypeptide protein
Length: 120
No structure alignment results are available for 2B8K.K explicitly.

It is represented by chain 1TWF.K which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1TWF.K

 
 
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To see how chain 2B8K.K compares with the representative chain d1twfk_ select a method below:





Entity #12: Chains: L
Description: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide protein
Length: 70
No structure alignment results are available for 2B8K.L explicitly.

It is represented by chain 4C2M.1 which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4C2M.1

 
 
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To see how chain 2B8K.L compares with the representative chain PDP:4C2M1_ select a method below:





Entity #2: Chains: B
Description: DNA-directed RNA polymerase II 140 kDa polypeptide protein
Length: 1224
No structure alignment results are available for 2B8K.B explicitly.

It is represented by chain 1TWF.B which is 100% sequence identical.

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

 
 
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To see how chain 2B8K.B compares with the representative chain d1twfb_ select a method below:





Entity #3: Chains: C
Description: DNA-directed RNA polymerase II 45 kDa polypeptide protein
Length: 318
No structure alignment results are available for 2B8K.C explicitly.

It is represented by chain 1TWF.C which is 100% sequence identical.

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

 
 
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To see how chain 2B8K.C compares with the representative chain d1twfc1 select a method below:





Entity #4: Chains: D
Description: DNA-directed RNA polymerase II 32 kDa polypeptide protein
Length: 221
No structure alignment results are available for 2B8K.D explicitly.

It is represented by chain 3PO2.D which is 100% sequence identical.

 Click here to show the structure comparison results for representative 3PO2.D

 
 
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To see how chain 2B8K.D compares with the representative chain PDP:3PO2Da select a method below:





Entity #5: Chains: E
Description: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide protein
Length: 215
No structure alignment results are available for 2B8K.E explicitly.

It is represented by chain 1DZF.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1DZF.A

 
 
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To see how chain 2B8K.E compares with the representative chain d1dzfa1 select a method below:





Entity #6: Chains: F
Description: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide protein
Length: 155
No structure alignment results are available for 2B8K.F explicitly.

It is represented by chain 4C2M.F which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4C2M.F

 
 
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To see how chain 2B8K.F compares with the representative chain PDP:4C2MFa select a method below:





Entity #7: Chains: G
Description: DNA-directed RNA polymerase II 19 kDa polypeptide protein
Length: 215
 
 
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Entity #8: Chains: H
Description: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide protein
Length: 146
No structure alignment results are available for 2B8K.H explicitly.

It is represented by chain 4C2M.H which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4C2M.H

 
 
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To see how chain 2B8K.H compares with the representative chain PDP:4C2MHa select a method below:





Entity #9: Chains: I
Description: DNA-directed RNA polymerase II subunit 9 protein
Length: 122
No structure alignment results are available for 2B8K.I explicitly.

It is represented by chain 1TWF.I which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1TWF.I

 
 
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To see how chain 2B8K.I compares with the representative chain d1twfi1 select a method below:





  • Update Status Hide
    Oct 14 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.