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RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID
4A3C

Structural Similarities for the Entities in PDB 4A3C

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 SUBUNIT RPB1 protein
Length: 1732
No structure alignment results are available for 4A3C.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 4A3C.A compares with the representative chain d1twfa_ select a method below:





Entity #10: Chains: J
Description: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 protein
Length: 70
No structure alignment results are available for 4A3C.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 4A3C.J compares with the representative chain PDP:4C2MJa select a method below:





Entity #11: Chains: K
Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 protein
Length: 120
No structure alignment results are available for 4A3C.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 4A3C.K compares with the representative chain d1twfk_ select a method below:





Entity #12: Chains: L
Description: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 protein
Length: 70
No structure alignment results are available for 4A3C.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 4A3C.L compares with the representative chain PDP:4C2M1_ select a method below:





Entity #13: Chains: N
Description: NON TEMPLATE DNA dna
Length: 14

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

 




Entity #14: Chains: P
Description: TRANSCRIPT RNA, 5'-R(*CP*AP*GP*GP*AP)-3' rna
Length: 5

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

 




Entity #15: Chains: T
Description: TEMPLATE DNA dna
Length: 26

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

 




Entity #2: Chains: B
Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 protein
Length: 1224
No structure alignment results are available for 4A3C.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 4A3C.B compares with the representative chain d1twfb_ select a method below:





Entity #3: Chains: C
Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 protein
Length: 318
No structure alignment results are available for 4A3C.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 4A3C.C compares with the representative chain d1twfc1 select a method below:





Entity #4: Chains: D
Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 protein
Length: 221
No structure alignment results are available for 4A3C.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 4A3C.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 SUBUNIT RPABC 1 protein
Length: 215
No structure alignment results are available for 4A3C.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 4A3C.E compares with the representative chain d1dzfa1 select a method below:





Entity #6: Chains: F
Description: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 protein
Length: 155
No structure alignment results are available for 4A3C.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 4A3C.F compares with the representative chain PDP:4C2MFa select a method below:





Entity #7: Chains: G
Description: RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 protein
Length: 171
No structure alignment results are available for 4A3C.G explicitly.

It is represented by chain 1Y14.B which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1Y14.B

 
 
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To see how chain 4A3C.G compares with the representative chain d1y14b1 select a method below:





Entity #8: Chains: H
Description: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 protein
Length: 146
No structure alignment results are available for 4A3C.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 4A3C.H compares with the representative chain PDP:4C2MHa select a method below:





Entity #9: Chains: I
Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 protein
Length: 122
No structure alignment results are available for 4A3C.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 4A3C.I compares with the representative chain d1twfi1 select a method below:





  • Update Status Hide
    Aug 26 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.