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Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Structural Similarities for the Entities in PDB 4IFD

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: Exosome complex component RRP45 protein
Length: 304

Entity #10: Chains: J
Description: Exosome complex exonuclease DIS3 protein
Length: 1003

Entity #11: Chains: K
Description: Exosome complex exonuclease RRP6 protein
Length: 179

Entity #12: Chains: R
Description: RNA (45-MER) rna
Length: 45

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


Entity #2: Chains: B
Description: Exosome complex component SKI6 protein
Length: 248

Entity #3: Chains: C
Description: Exosome complex component RRP43 protein
Length: 393

Entity #4: Chains: D
Description: Exosome complex component RRP46 protein
Length: 245

Entity #5: Chains: E
Description: Exosome complex component RRP42 protein
Length: 267

Entity #6: Chains: F
Description: Exosome complex component MTR3 protein
Length: 250

Entity #7: Chains: G
Description: Exosome complex component RRP40 protein
Length: 242

Entity #8: Chains: H
Description: Exosome complex component RRP4 protein
Length: 361

Entity #9: Chains: I
Description: Exosome complex component CSL4 protein
Length: 301

  • Update Status Hide
    Mar 17 2015

    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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