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STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FROM MOLECULE I.
2J01

Structural Similarities for the Entities in PDB 2J01

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: 0
Description: 50S RIBOSOMAL PROTEIN L27 protein
Length: 85
No structure alignment results are available for 2J01.0 explicitly.

It is represented by chain 1V8Q.A which is 100% sequence identical.

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Entity #10: Chains: A
Description: 23S RIBOSOMAL RNA rna
Length: 2787

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

 




Entity #11: Chains: B
Description: 5S RIBOSOMAL RNA rna
Length: 122

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

 




Entity #12: Chains: C
Description: 50S RIBOSOMAL PROTEIN L1 protein
Length: 229
No structure alignment results are available for 2J01.C explicitly.

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

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Entity #13: Chains: D
Description: 50S RIBOSOMAL PROTEIN L2 protein
Length: 276
No structure alignment results are available for 2J01.D explicitly.

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

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Entity #14: Chains: E
Description: 50S RIBOSOMAL PROTEIN L3 protein
Length: 206
No structure alignment results are available for 2J01.E explicitly.

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

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Entity #15: Chains: F
Description: 50S RIBOSOMAL PROTEIN L4 protein
Length: 210
No structure alignment results are available for 2J01.F explicitly.

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

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Entity #16: Chains: G
Description: 50S RIBOSOMAL PROTEIN L5 protein
Length: 182
No structure alignment results are available for 2J01.G explicitly.

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

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Entity #17: Chains: H
Description: 50S RIBOSOMAL PROTEIN L6 protein
Length: 180
No structure alignment results are available for 2J01.H explicitly.

It is represented by chain 1RL6.A which has more than 50% sequence identity.

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

 
 
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Entity #18: Chains: I
Description: 50S RIBOSOMAL PROTEIN L9 protein
Length: 148
No structure alignment results are available for 2J01.I explicitly.

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

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Entity #19: Chains: N
Description: 50S RIBOSOMAL PROTEIN L13 protein
Length: 140
No structure alignment results are available for 2J01.N explicitly.

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

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Entity #2: Chains: 1
Description: 50S RIBOSOMAL PROTEIN L28 protein
Length: 98
No structure alignment results are available for 2J01.1 explicitly.

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

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Entity #20: Chains: O
Description: 50S RIBOSOMAL PROTEIN L14 protein
Length: 122
No structure alignment results are available for 2J01.O explicitly.

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

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

 
 
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Entity #21: Chains: P
Description: 50S RIBOSOMAL PROTEIN L15 protein
Length: 150
No structure alignment results are available for 2J01.P explicitly.

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

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Entity #22: Chains: Q
Description: 50S RIBOSOMAL PROTEIN L16 protein
Length: 141
No structure alignment results are available for 2J01.Q explicitly.

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

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Entity #23: Chains: R
Description: 50S RIBOSOMAL PROTEIN L17 protein
Length: 118
No structure alignment results are available for 2J01.R explicitly.

It is represented by chain 1GD8.A which is 100% sequence identical.

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Entity #24: Chains: S
Description: 50S RIBOSOMAL PROTEIN L18 protein
Length: 112
No structure alignment results are available for 2J01.S explicitly.

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

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Entity #25: Chains: T
Description: 50S RIBOSOMAL PROTEIN L19 protein
Length: 146
No structure alignment results are available for 2J01.T explicitly.

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

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Entity #26: Chains: U
Description: 50S RIBOSOMAL PROTEIN L20 protein
Length: 118
No structure alignment results are available for 2J01.U explicitly.

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

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Entity #27: Chains: V
Description: 50S RIBOSOMAL PROTEIN L21 protein
Length: 101
No structure alignment results are available for 2J01.V explicitly.

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

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Entity #28: Chains: W
Description: 50S RIBOSOMAL PROTEIN L22 protein
Length: 113
No structure alignment results are available for 2J01.W explicitly.

It is represented by chain 1I4J.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 1I4J.A

 
 
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Entity #29: Chains: X
Description: 50S RIBOSOMAL PROTEIN L23 protein
Length: 96
No structure alignment results are available for 2J01.X explicitly.

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

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Entity #3: Chains: 2
Description: 50S RIBOSOMAL PROTEIN L29 protein
Length: 72
No structure alignment results are available for 2J01.2 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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Entity #30: Chains: Y
Description: 50S RIBOSOMAL PROTEIN L24 protein
Length: 110
No structure alignment results are available for 2J01.Y 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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Entity #31: Chains: Z
Description: 50S RIBOSOMAL PROTEIN L25 protein
Length: 206
No structure alignment results are available for 2J01.Z explicitly.

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

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

 
 
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Entity #32: Chains: 9
Description: 50S RIBOSOMAL PROTEIN L36 protein
Length: 37
No structure alignment results are available for 2J01.9 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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Entity #33: Chains: J
Description: 50S RIBOSOMAL PROTEIN L10 protein
Length: 173
No structure alignment results are available for 2J01.J explicitly.

It is represented by chain 3I8I.Y which is 100% sequence identical.

 Click here to show the structure comparison results for representative 3I8I.Y

 
 
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Entity #34: Chains: K
Description: 50S RIBOSOMAL PROTEIN L11 protein
Length: 147
No structure alignment results are available for 2J01.K explicitly.

It is represented by chain 3EGV.B which has more than 95% sequence identity.

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

 
 
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Entity #35: Chains: L,M
Description: 50S RIBOSOMAL PROTEIN L7 protein
Length: 125
No structure alignment results are available for 2J01.L, 2J01.M explicitly.

These chains are represented by chain 1DD3.A which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 1DD3.A

 
 
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Entity #4: Chains: 3
Description: 50S RIBOSOMAL PROTEIN L30 protein
Length: 60
No structure alignment results are available for 2J01.3 explicitly.

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

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

 
 
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Entity #5: Chains: 4
Description: 50S RIBOSOMAL PROTEIN L31 protein
Length: 71
No structure alignment results are available for 2J01.4 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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Entity #6: Chains: 5
Description: 50S RIBOSOMAL PROTEIN L32 protein
Length: 60
No structure alignment results are available for 2J01.5 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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Entity #7: Chains: 6
Description: 50S RIBOSOMAL PROTEIN L33 protein
Length: 54
No structure alignment results are available for 2J01.6 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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Entity #8: Chains: 7
Description: 50S RIBOSOMAL PROTEIN L34 protein
Length: 49
No structure alignment results are available for 2J01.7 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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Entity #9: Chains: 8
Description: 50S RIBOSOMAL PROTEIN L35 protein
Length: 65
No structure alignment results are available for 2J01.8 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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  • 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.

     
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Documentation

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