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70S Ribosome translocation intermediate FA-3.6A CONTAINING ELONGATION FACTOR EFG/FUSIDIC ACID/GDP, MRNA, AND TRNA BOUND IN THE pe*/E STATE. THIS ENTRY CONTAINS THE 30S RIBOSOMAL SUBUNIT A. THE 50S SUBUNIT A CAN BE FOUND IN 4KD9. MOLECULE B IN THE SAME ASYMMETRIC UNIT IS DEPOSITED AS 4KDA (30S) AND 4KDB (50S).
4KD8

Structural Similarities for the Entities in PDB 4KD8

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: B
Description: 30S ribosomal protein S2 protein
Length: 235
No structure alignment results are available for 4KD8.B explicitly.

It is represented by chain 4RB5.B which is 100% sequence identical.

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Entity #10: Chains: K
Description: 30S ribosomal protein S11 protein
Length: 119
No structure alignment results are available for 4KD8.K explicitly.

It is represented by chain 4CVN.E which has more than 40% sequence identity.

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Entity #11: Chains: L
Description: 30S ribosomal protein S12 protein
Length: 125
No structure alignment results are available for 4KD8.L explicitly.

It is represented by chain 4RB5.L which is 100% sequence identical.

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Entity #12: Chains: M
Description: 30S ribosomal protein S13 protein
Length: 125
No structure alignment results are available for 4KD8.M explicitly.

It is represented by chain 4RB5.M which is 100% sequence identical.

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Entity #13: Chains: N
Description: 30S ribosomal protein S14 type Z protein
Length: 60
No structure alignment results are available for 4KD8.N explicitly.

It is represented by chain 4RB5.N which is 100% sequence identical.

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Entity #14: Chains: O
Description: 30S ribosomal protein S15 protein
Length: 88
No structure alignment results are available for 4KD8.O explicitly.

It is represented by chain 4A5U.B which has more than 95% sequence identity.

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Entity #15: Chains: P
Description: 30S ribosomal protein S16 protein
Length: 84
No structure alignment results are available for 4KD8.P explicitly.

It is represented by chain 4RB5.P which is 100% sequence identical.

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Entity #16: Chains: Q
Description: 30S ribosomal protein S17 protein
Length: 100
No structure alignment results are available for 4KD8.Q explicitly.

It is represented by chain 4RB5.Q which is 100% sequence identical.

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Entity #17: Chains: R
Description: 30S ribosomal protein S18 protein
Length: 70
No structure alignment results are available for 4KD8.R explicitly.

It is represented by chain 4JYA.R which is 100% sequence identical.

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Entity #18: Chains: S
Description: 30S ribosomal protein S19 protein
Length: 79
No structure alignment results are available for 4KD8.S explicitly.

It is represented by chain 3A1P.B which has more than 50% sequence identity.

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Entity #19: Chains: T
Description: 30S ribosomal protein S20 protein
Length: 99
No structure alignment results are available for 4KD8.T explicitly.

It is represented by chain 4RB5.T which is 100% sequence identical.

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Entity #2: Chains: C
Description: 30S ribosomal protein S3 protein
Length: 207
No structure alignment results are available for 4KD8.C explicitly.

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

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Entity #20: Chains: A
Description: ribosomal RNA 16S rna
Length: 1511

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

 




Entity #21: Chains: W
Description: transfer RNA rna
Length: 77

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

 




Entity #22: Chains: V
Description: messenger RNA rna
Length: 23

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

 




Entity #23: Chains: Y
Description: Elongation factor G protein
Length: 687
No structure alignment results are available for 4KD8.Y explicitly.

It is represented by chain 2XEX.A which has more than 50% sequence identity.

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Entity #24: Chains: U
Description: VIOMYCIN protein
Length: 6

This entity is too short to be considered for the all vs. all structure alignments.

 




Entity #3: Chains: D
Description: 30S ribosomal protein S4 protein
Length: 208
No structure alignment results are available for 4KD8.D explicitly.

It is represented by chain 4RB5.D which is 100% sequence identical.

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Entity #4: Chains: E
Description: 30S ribosomal protein S5 protein
Length: 151
No structure alignment results are available for 4KD8.E explicitly.

It is represented by chain 4RB5.E which is 100% sequence identical.

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Entity #5: Chains: F
Description: 30S ribosomal protein S6 protein
Length: 101
No structure alignment results are available for 4KD8.F explicitly.

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

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Entity #6: Chains: G
Description: 30S ribosomal protein S7 protein
Length: 155
No structure alignment results are available for 4KD8.G explicitly.

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

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Entity #7: Chains: H
Description: 30S ribosomal protein S8 protein
Length: 138
No structure alignment results are available for 4KD8.H explicitly.

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

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Entity #8: Chains: I
Description: 30S ribosomal protein S9 protein
Length: 127
No structure alignment results are available for 4KD8.I explicitly.

It is represented by chain 4RB5.I which is 100% sequence identical.

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Entity #9: Chains: J
Description: 30S ribosomal protein S10 protein
Length: 99
No structure alignment results are available for 4KD8.J explicitly.

It is represented by chain 3D3B.J which has more than 50% sequence identity.

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  • 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.