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Crystal structure of the entire respiratory complex I from Thermus thermophilus
4HEA

Structural Similarities for the Entities in PDB 4HEA

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: 1,B
Description: NADH-quinone oxidoreductase subunit 1 protein
Length: 438
 
 
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Entity #10: Chains: A,P
Description: NADH-quinone oxidoreductase subunit 7 protein
Length: 119
 
 
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Entity #11: Chains: J,R
Description: NADH-quinone oxidoreductase subunit 10 protein
Length: 176
 
 
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Entity #12: Chains: K,S
Description: NADH-quinone oxidoreductase subunit 11 protein
Length: 95
 
 
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Entity #13: Chains: L,T
Description: NADH-quinone oxidoreductase subunit 12 protein
Length: 606
No structure alignment results are available for 4HEA.L, 4HEA.T explicitly.

These chains are represented by chain 3RKO.B which has more than 40% sequence identity.

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

 
 
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To see how chain 4HEA.T compares with the representative chain PDP:3RKOBa select a method below:





Entity #14: Chains: M,U
Description: NADH-quinone oxidoreductase subunit 13 protein
Length: 469
 
 
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Entity #15: Chains: N,V
Description: NADH-quinone oxidoreductase subunit 14 protein
Length: 427
 
 
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Entity #16: Chains: H,Q
Description: NADH-quinone oxidoreductase subunit 8 protein
Length: 365
 
 
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Entity #2: Chains: 2,C
Description: NADH-quinone oxidoreductase subunit 2 protein
Length: 181
 
 
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Entity #3: Chains: 3,D
Description: NADH-quinone oxidoreductase subunit 3 protein
Length: 783
 
 
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Entity #4: Chains: 4,E
Description: NADH-quinone oxidoreductase subunit 4 protein
Length: 409
 
 
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Entity #5: Chains: 5,F
Description: NADH-quinone oxidoreductase subunit 5 protein
Length: 207
 
 
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Entity #6: Chains: 6,G
Description: NADH-quinone oxidoreductase subunit 6 protein
Length: 181
 
 
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Entity #7: Chains: 9,O
Description: NADH-quinone oxidoreductase subunit 9 protein
Length: 182
 
 
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Entity #8: Chains: 7,I
Description: NADH-quinone oxidoreductase subunit 15 protein
Length: 129
 
 
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Entity #9: Chains: W,X
Description: Putative uncharacterized protein TTHA1528 protein
Length: 131
No structure alignment results are available for 4HEA.W, 4HEA.X explicitly.

These chains are represented by chain 1WNA.A which is 100% sequence identical.

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

 
 
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To see how chain 4HEA.X compares with the representative chain d1wnaa1 select a method below:





  • Update Status Hide
    Nov 18 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.

     
Comparison Tool

Calculate pairwise sequence or structure alignments.

PDB 1: Chain 1: ...
PDB 2: Chain 2: ...
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Documentation

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