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Control of ribosomal subunit rotation by elongation factor G
4KJ3

Structural Similarities for the Entities in PDB 4KJ3

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: 5S rRNA rna
Length: 120

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

 




Entity #10: Chains: J
Description: 50S ribosomal protein L13 protein
Length: 142
No structure alignment results are available for 4KJ3.J explicitly.

It is represented by chain 4QCN.N which has more than 50% sequence identity.

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Entity #11: Chains: K
Description: 50S ribosomal protein L14 protein
Length: 123
No structure alignment results are available for 4KJ3.K explicitly.

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

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Entity #12: Chains: L
Description: 50S ribosomal protein L15 protein
Length: 144
No structure alignment results are available for 4KJ3.L explicitly.

It is represented by chain 4QCN.P which has more than 40% sequence identity.

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Entity #13: Chains: M
Description: 50S ribosomal protein L16 protein
Length: 136
No structure alignment results are available for 4KJ3.M explicitly.

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

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Entity #14: Chains: N
Description: 50S ribosomal protein L17 protein
Length: 127
No structure alignment results are available for 4KJ3.N explicitly.

It is represented by chain 1GD8.A which has more than 50% sequence identity.

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Entity #15: Chains: O
Description: 50S ribosomal protein L18 protein
Length: 117
No structure alignment results are available for 4KJ3.O explicitly.

It is represented by chain 4QCN.S which has more than 50% sequence identity.

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Entity #16: Chains: P
Description: 50S ribosomal protein L19 protein
Length: 115
No structure alignment results are available for 4KJ3.P explicitly.

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

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Entity #17: Chains: Q
Description: 50S ribosomal protein L20 protein
Length: 118
No structure alignment results are available for 4KJ3.Q explicitly.

It is represented by chain 4QCN.U which has more than 50% sequence identity.

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Entity #18: Chains: R
Description: 50S ribosomal protein L21 protein
Length: 103
No structure alignment results are available for 4KJ3.R explicitly.

It is represented by chain 4QCN.V which has more than 40% sequence identity.

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Entity #19: Chains: S
Description: 50S ribosomal protein L22 protein
Length: 110
No structure alignment results are available for 4KJ3.S explicitly.

It is represented by chain 1I4J.A which has more than 50% sequence identity.

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Entity #2: Chains: A
Description: 23S rRNA rna
Length: 2904

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

 




Entity #20: Chains: T
Description: 50S ribosomal protein L23 protein
Length: 100
No structure alignment results are available for 4KJ3.T explicitly.

It is represented by chain 4QCN.X which has more than 40% sequence identity.

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Entity #21: Chains: U
Description: 50S ribosomal protein L24 protein
Length: 104
No structure alignment results are available for 4KJ3.U explicitly.

It is represented by chain 4QCN.Y which has more than 40% sequence identity.

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Entity #22: Chains: V
Description: 50S ribosomal protein L25 protein
Length: 94
No structure alignment results are available for 4KJ3.V explicitly.

It is represented by chain 1DFU.P which is 100% sequence identical.

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Entity #23: Chains: W
Description: 50S ribosomal protein L27 protein
Length: 85
No structure alignment results are available for 4KJ3.W explicitly.

It is represented by chain 1V8Q.A which has more than 50% sequence identity.

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Entity #24: Chains: X
Description: 50S ribosomal protein L28 protein
Length: 78
No structure alignment results are available for 4KJ3.X explicitly.

It is represented by chain 4TPD.X which is 100% sequence identical.

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Entity #25: Chains: Y
Description: 50S ribosomal protein L29 protein
Length: 63
No structure alignment results are available for 4KJ3.Y explicitly.

It is represented by chain 4QCN.2 which has more than 40% sequence identity.

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Entity #26: Chains: Z
Description: 50S ribosomal protein L30 protein
Length: 59
No structure alignment results are available for 4KJ3.Z explicitly.

It is represented by chain 1BXY.A which has more than 40% sequence identity.

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Entity #27: Chains: 0
Description: 50S ribosomal protein L32 protein
Length: 57
No structure alignment results are available for 4KJ3.0 explicitly.

It is represented by chain 4QCN.5 which has more than 40% sequence identity.

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Entity #28: Chains: 1
Description: 50S ribosomal protein L33 protein
Length: 55
No structure alignment results are available for 4KJ3.1 explicitly.

It is represented by chain 4QCN.6 which has more than 40% sequence identity.

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Entity #29: Chains: 2
Description: 50S ribosomal protein L34 protein
Length: 46
No structure alignment results are available for 4KJ3.2 explicitly.

It is represented by chain 4TPD.2 which is 100% sequence identical.

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Entity #3: Chains: C
Description: 50S ribosomal protein L2 protein
Length: 273
No structure alignment results are available for 4KJ3.C explicitly.

It is represented by chain 4QCN.D which has more than 50% sequence identity.

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Entity #30: Chains: 3
Description: 50S ribosomal protein L35 protein
Length: 65
No structure alignment results are available for 4KJ3.3 explicitly.

It is represented by chain 4TPD.3 which is 100% sequence identical.

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Entity #31: Chains: 4
Description: 50S ribosomal protein L36 protein
Length: 38
No structure alignment results are available for 4KJ3.4 explicitly.

It is represented by chain 4QCN.9 which has more than 50% sequence identity.

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Entity #4: Chains: D
Description: 50S ribosomal protein L3 protein
Length: 209
No structure alignment results are available for 4KJ3.D explicitly.

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

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Entity #5: Chains: E
Description: 50S ribosomal protein L4 protein
Length: 201
No structure alignment results are available for 4KJ3.E explicitly.

It is represented by chain 1DMG.A which has more than 40% sequence identity.

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Entity #6: Chains: F
Description: 50S ribosomal protein L5 protein
Length: 179
No structure alignment results are available for 4KJ3.F explicitly.

It is represented by chain 1IQ4.A which has more than 50% sequence identity.

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Entity #7: Chains: G
Description: 50S ribosomal protein L6 protein
Length: 177
No structure alignment results are available for 4KJ3.G explicitly.

It is represented by chain 1RL6.A which has more than 40% sequence identity.

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Entity #8: Chains: H
Description: 50S ribosomal protein L9 protein
Length: 50
No structure alignment results are available for 4KJ3.H explicitly.

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

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Entity #9: Chains: I
Description: 50S ribosomal protein L11 protein
Length: 142
No structure alignment results are available for 4KJ3.I explicitly.

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

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  • Update Status Hide
    Sep 02 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.

     
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Documentation

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