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CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI AT 2.4 ANGSTROM RESOLUTION
1FFK

Structural Similarities for the Entities in PDB 1FFK

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: 23S RRNA rna
Length: 2922

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

 




Entity #10: Chains: H
Description: RIBOSOMAL PROTEIN L14 protein
Length: 132
No structure alignment results are available for 1FFK.H explicitly.

It is represented by chain 4HUB.K which is 100% sequence identical.

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Entity #11: Chains: I
Description: RIBOSOMAL PROTEIN L15E protein
Length: 194
No structure alignment results are available for 1FFK.I explicitly.

It is represented by chain 4HUB.M which has more than 70% sequence identity.

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Entity #12: Chains: J
Description: RIBOSOMAL PROTEIN L15 protein
Length: 164
No structure alignment results are available for 1FFK.J explicitly.

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

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Entity #13: Chains: K
Description: RIBOSOMAL PROTEIN L18 protein
Length: 186
No structure alignment results are available for 1FFK.K explicitly.

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

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Entity #14: Chains: L
Description: RIBOSOMAL PROTEIN L18E protein
Length: 115
No structure alignment results are available for 1FFK.L explicitly.

It is represented by chain 4HUB.O which is 100% sequence identical.

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Entity #15: Chains: M
Description: RIBOSOMAL PROTEIN L19 protein
Length: 148
No structure alignment results are available for 1FFK.M explicitly.

It is represented by chain 4HUB.P which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.P

 
 
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Entity #16: Chains: N
Description: RIBOSOMAL PROTEIN L21E protein
Length: 95
No structure alignment results are available for 1FFK.N explicitly.

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

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Entity #17: Chains: O
Description: RIBOSOMAL PROTEIN L22 protein
Length: 154
No structure alignment results are available for 1FFK.O explicitly.

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

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Entity #18: Chains: P
Description: RIBOSOMAL PROTEIN L23 protein
Length: 84
No structure alignment results are available for 1FFK.P explicitly.

It is represented by chain 4HUB.S which is 100% sequence identical.

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Entity #19: Chains: Q
Description: RIBOSOMAL PROTEIN L24 protein
Length: 119
No structure alignment results are available for 1FFK.Q explicitly.

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

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Entity #2: Chains: 9
Description: 5S RRNA rna
Length: 122

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

 




Entity #20: Chains: R
Description: RIBOSOMAL PROTEIN L24E protein
Length: 66
No structure alignment results are available for 1FFK.R explicitly.

It is represented by chain 4HUB.U which is 100% sequence identical.

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Entity #21: Chains: S
Description: RIBOSOMAL PROTEIN L29 protein
Length: 70
No structure alignment results are available for 1FFK.S explicitly.

It is represented by chain 4HUB.V which is 100% sequence identical.

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Entity #22: Chains: T
Description: RIBOSOMAL PROTEIN L30 protein
Length: 154
No structure alignment results are available for 1FFK.T explicitly.

It is represented by chain 4HUB.W which is 100% sequence identical.

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Entity #23: Chains: U
Description: RIBOSOMAL PROTEIN L31E protein
Length: 91
No structure alignment results are available for 1FFK.U explicitly.

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

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Entity #24: Chains: V
Description: RIBOSOMAL PROTEIN L32E protein
Length: 143
No structure alignment results are available for 1FFK.V explicitly.

It is represented by chain 3G6E.Y which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 3G6E.Y

 
 
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Entity #25: Chains: W
Description: RIBOSOMAL PROTEIN L37AE protein
Length: 73
No structure alignment results are available for 1FFK.W explicitly.

It is represented by chain 1S72.Z which has more than 50% sequence identity.

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Entity #26: Chains: X
Description: RIBOSOMAL PROTEIN L37E protein
Length: 56
No structure alignment results are available for 1FFK.X explicitly.

It is represented by chain 4HUB.1 which is 100% sequence identical.

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Entity #27: Chains: Y
Description: RIBOSOMAL PROTEIN L39E protein
Length: 49
No structure alignment results are available for 1FFK.Y explicitly.

It is represented by chain 4HUB.2 which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.2

 
 
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Entity #28: Chains: Z
Description: RIBOSOMAL PROTEIN L44E protein
Length: 92
No structure alignment results are available for 1FFK.Z explicitly.

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

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Entity #29: Chains: 1
Description: RIBOSOMAL PROTEIN L6 protein
Length: 177
No structure alignment results are available for 1FFK.1 explicitly.

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

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Entity #3: Chains: A
Description: RIBOSOMAL PROTEIN L2 protein
Length: 239
No structure alignment results are available for 1FFK.A explicitly.

It is represented by chain 4HUB.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.A

 
 
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Entity #4: Chains: B
Description: RIBOSOMAL PROTEIN L3 protein
Length: 337
No structure alignment results are available for 1FFK.B explicitly.

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

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

 
 
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Entity #5: Chains: C
Description: RIBOSOMAL PROTEIN L4 protein
Length: 246
No structure alignment results are available for 1FFK.C explicitly.

It is represented by chain 4HUB.C which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.C

 
 
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Entity #6: Chains: D
Description: RIBOSOMAL PROTEIN L5 protein
Length: 176
No structure alignment results are available for 1FFK.D explicitly.

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

 Click here to show the structure comparison results for representative 4HUB.D

 
 
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Entity #7: Chains: E
Description: RIBOSOMAL PROTEIN L7AE protein
Length: 119
No structure alignment results are available for 1FFK.E explicitly.

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

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

 
 
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Entity #8: Chains: F
Description: RIBOSOMAL PROTEIN L10E protein
Length: 157
No structure alignment results are available for 1FFK.F explicitly.

It is represented by chain 4HUB.H which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.H

 
 
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Entity #9: Chains: G
Description: RIBOSOMAL PROTEIN L13 protein
Length: 145
No structure alignment results are available for 1FFK.G explicitly.

It is represented by chain 1J3A.A which has more than 40% sequence identity.

 Click here to show the structure comparison results for representative 1J3A.A

 
 
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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.