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An Information Portal to 105097 Biological Macromolecular Structures

Coordinates of S12, L11 proteins and E-site tRNA from 70S crystal structure separately fitted into the Cryo-EM map of E.coli 70S.EF-G.GDPNP complex. The atomic coordinates originally from the E-site tRNA were fitted in the position of the hybrid P/E-site tRNA.
1PN8

Structural Similarities for the Entities in PDB 1PN8

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: D
Description: E-tRNA rna
Length: 68

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

 




Entity #2: Chains: O
Description: 30S ribosomal protein S12 protein
Length: 124
No structure alignment results are available for 1PN8.O explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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To see how chain 1PN8.O compares with the representative chain xxxx select a method below:





Entity #3: Chains: L
Description: 50S ribosomal protein L11 protein
Length: 133
No structure alignment results are available for 1PN8.L 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 1PN8.L compares with the representative chain d3egvb1 select a method below:





  • Update Status Hide
    Dec 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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PDB 1: Chain 1: ...
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Documentation

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