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Co-cystal of large Ribosomal Subunit mutant G2616A with CC-Puromycin
3CD6

Structural Similarities for the Entities in PDB 3CD6

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: A
Description: 50S ribosomal protein L2P protein
Length: 240
No structure alignment results are available for 3CD6.A explicitly.

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

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Entity #10: Chains: J
Description: 50S ribosomal protein L13P protein
Length: 145
No structure alignment results are available for 3CD6.J explicitly.

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

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Entity #11: Chains: K
Description: 50S ribosomal protein L14P protein
Length: 132
No structure alignment results are available for 3CD6.K explicitly.

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

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Entity #12: Chains: L
Description: 50S ribosomal protein L15P protein
Length: 165
No structure alignment results are available for 3CD6.L explicitly.

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

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Entity #13: Chains: M
Description: 50S ribosomal protein L15e protein
Length: 196
No structure alignment results are available for 3CD6.M explicitly.

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

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Entity #14: Chains: N
Description: 50S ribosomal protein L18P protein
Length: 187
No structure alignment results are available for 3CD6.N explicitly.

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

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Entity #15: Chains: O
Description: 50S ribosomal protein L18e protein
Length: 116
No structure alignment results are available for 3CD6.O explicitly.

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

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Entity #16: Chains: P
Description: 50S ribosomal protein L19e protein
Length: 149
No structure alignment results are available for 3CD6.P explicitly.

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

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Entity #17: Chains: Q
Description: 50S ribosomal protein L21e protein
Length: 96
No structure alignment results are available for 3CD6.Q explicitly.

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

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Entity #18: Chains: R
Description: 50S ribosomal protein L22P protein
Length: 155
No structure alignment results are available for 3CD6.R explicitly.

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

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Entity #19: Chains: S
Description: 50S ribosomal protein L23P protein
Length: 85
No structure alignment results are available for 3CD6.S explicitly.

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

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Entity #2: Chains: B
Description: 50S ribosomal protein L3P protein
Length: 338
No structure alignment results are available for 3CD6.B explicitly.

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

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Entity #20: Chains: T
Description: 50S ribosomal protein L24P protein
Length: 120
No structure alignment results are available for 3CD6.T explicitly.

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

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Entity #21: Chains: U
Description: 50S ribosomal protein L24e protein
Length: 67
No structure alignment results are available for 3CD6.U explicitly.

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

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Entity #22: Chains: V
Description: 50S ribosomal protein L29P protein
Length: 71
No structure alignment results are available for 3CD6.V explicitly.

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

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Entity #23: Chains: W
Description: 50S ribosomal protein L30P protein
Length: 154
No structure alignment results are available for 3CD6.W explicitly.

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

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Entity #24: Chains: X
Description: 50S ribosomal protein L31e protein
Length: 92
No structure alignment results are available for 3CD6.X explicitly.

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

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Entity #25: Chains: Y
Description: 50S ribosomal protein L32e protein
Length: 241
No structure alignment results are available for 3CD6.Y explicitly.

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

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Entity #26: Chains: Z
Description: 50S ribosomal protein L37Ae protein
Length: 116
No structure alignment results are available for 3CD6.Z explicitly.

It is represented by chain 3CC2.Z which is 100% sequence identical.

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Entity #27: Chains: 1
Description: 50S ribosomal protein L37e protein
Length: 57
No structure alignment results are available for 3CD6.1 explicitly.

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

 Click here to show the structure comparison results for representative 4HUB.1

 
 
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Entity #28: Chains: 2
Description: 50S ribosomal protein L39e protein
Length: 50
No structure alignment results are available for 3CD6.2 explicitly.

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

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Entity #29: Chains: 3
Description: 50S ribosomal protein L44E protein
Length: 92
No structure alignment results are available for 3CD6.3 explicitly.

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

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Entity #3: Chains: C
Description: 50S ribosomal protein L4P protein
Length: 246
No structure alignment results are available for 3CD6.C explicitly.

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

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Entity #30: Chains: 0
Description: 23S RIBOSOMAL RNA rna
Length: 2923

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

 




Entity #31: Chains: 9
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 #32: Chains: 4
Description: RNA (5'-R(*CP*CP*(PPU))-3') rna
Length: 3

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

 




Entity #4: Chains: D
Description: 50S ribosomal protein L5P protein
Length: 177
No structure alignment results are available for 3CD6.D explicitly.

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

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Entity #5: Chains: E
Description: 50S ribosomal protein L6P protein
Length: 178
No structure alignment results are available for 3CD6.E explicitly.

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

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Entity #6: Chains: F
Description: 50S ribosomal protein L7Ae protein
Length: 120
No structure alignment results are available for 3CD6.F 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 #7: Chains: G
Description: 50S ribosomal protein L10E protein
Length: 348
No structure alignment results are available for 3CD6.G explicitly.

It is represented by chain 1VQO.G which has more than 95% sequence identity.

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Entity #8: Chains: H
Description: 50S ribosomal protein L10e protein
Length: 177
No structure alignment results are available for 3CD6.H explicitly.

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

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

 
 
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Entity #9: Chains: I
Description: 50S ribosomal protein L11P protein
Length: 162
No structure alignment results are available for 3CD6.I explicitly.

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

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

 
 
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  • Update Status Hide
    Sep 09 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.