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FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME
1EG0

Structural Similarities for the Entities in PDB 1EG0

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: I
Description: FRAGMENT OF 16S RRNA HELIX 23 rna
Length: 33

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

 




Entity #10: Chains: F
Description: PROTEIN (S15 RIBOSOMAL PROTEIN) protein
Length: 89
No structure alignment results are available for 1EG0.F explicitly.

It is represented by chain 4A5U.B which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 4A5U.B

 
 
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To see how chain 1EG0.F compares with the representative chain PDP:4A5UBa select a method below:





Entity #11: Chains: G
Description: PROTEIN (S17 RIBOSOMAL PROTEIN) protein
Length: 93
No structure alignment results are available for 1EG0.G explicitly.

It is represented by chain 4TPC.Q which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 4TPC.Q

 
 
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To see how chain 1EG0.G compares with the representative chain PDP:4TPCQa select a method below:





Entity #12: Chains: H
Description: PROTEIN (S20 RIBOSOMAL PROTEIN) protein
Length: 100
Entity #13: Chains: N
Description: PROTEIN (RIBOSOMAL PROTEIN L1) protein
Length: 229
No structure alignment results are available for 1EG0.N explicitly.

It is represented by chain 3U42.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 3U42.A

 
 
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To see how chain 1EG0.N compares with the representative chain PDP:3U42Aa select a method below:





Entity #14: Chains: J
Description: PROTEIN (RIBOSOMAL PROTEIN L6) protein
Length: 171
No structure alignment results are available for 1EG0.J explicitly.

It is represented by chain 1RL6.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1RL6.A

 
 
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To see how chain 1EG0.J compares with the representative chain d1rl6a1 select a method below:





Entity #15: Chains: K
Description: PROTEIN (RIBOSOMAL PROTEIN L11) protein
Length: 140
No structure alignment results are available for 1EG0.K explicitly.

It is represented by chain 3EGV.B which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 3EGV.B

 
 
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To see how chain 1EG0.K compares with the representative chain d3egvb1 select a method below:





Entity #2: Chains: L
Description: FRAGMENT OF 23S RRNA rna
Length: 57

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

 




Entity #3: Chains: M
Description: HELIX 95 OF 23S RRNA rna
Length: 26

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

 




Entity #4: Chains: O
Description: FORMYL-METHIONYL-TRNA rna
Length: 76

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

 




Entity #5: Chains: A
Description: PROTEIN (S4 RIBOSOMAL PROTEIN) protein
Length: 159
 
 
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Entity #6: Chains: B
Description: PROTEIN (S5 RIBOSOMAL PROTEIN) protein
Length: 148
No structure alignment results are available for 1EG0.B explicitly.

It is represented by chain 4LFB.E which has more than 50% sequence identity.

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

 
 
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To see how chain 1EG0.B compares with the representative chain PDP:4LFBEa select a method below:





Entity #7: Chains: C
Description: PROTEIN (S6 RIBOSOMAL PROTEIN) protein
Length: 97
No structure alignment results are available for 1EG0.C explicitly.

It is represented by chain 1CQM.A which has more than 95% sequence identity.

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

 
 
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To see how chain 1EG0.C compares with the representative chain d1cqma_ select a method below:





Entity #8: Chains: D
Description: PROTEIN (S7 RIBOSOMAL PROTEIN) protein
Length: 146
No structure alignment results are available for 1EG0.D explicitly.

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

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

 
 
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To see how chain 1EG0.D compares with the representative chain d1rssa_ select a method below:





Entity #9: Chains: E
Description: PROTEIN (S8 RIBOSOMAL PROTEIN) protein
Length: 138
No structure alignment results are available for 1EG0.E explicitly.

It is represented by chain 1SEI.A which has more than 50% sequence identity.

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

 
 
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To see how chain 1EG0.E compares with the representative chain d1seia_ select a method below:





  • Update Status Hide
    Sep 16 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.