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Crystal Structure of Cytochrome b6f Complex from M.laminosus
1VF5

Structural Similarities for the Entities in PDB 1VF5

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,N
Description: CYTOCHROME B6 protein
Length: 215
No structure alignment results are available for 1VF5.A, 1VF5.N explicitly.

These chains are represented by chain 4OGQ.A which has more than 95% sequence identity.

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

 
 
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To see how chain 1VF5.N compares with the representative chain PDP:4OGQAa select a method below:





Entity #2: Chains: B,O
Description: SUBUNIT IV protein
Length: 160
No structure alignment results are available for 1VF5.B, 1VF5.O explicitly.

These chains are represented by chain 4OGQ.B which has more than 90% sequence identity.

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

 
 
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To see how chain 1VF5.O compares with the representative chain PDP:4OGQBa select a method below:





Entity #3: Chains: C,P
Description: CYTOCHROME F protein
Length: 289
No structure alignment results are available for 1VF5.C, 1VF5.P explicitly.

These chains are represented by chain 4H44.C which has more than 70% sequence identity.

 Click here to show the structure comparison results for representative 4H44.C

 
 
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To see how chain 1VF5.P compares with the representative chain PDP:4H44Ca select a method below:





Entity #4: Chains: D,Q
Description: RIESKE IRON-SULFUR PROTEIN protein
Length: 179
No structure alignment results are available for 1VF5.D, 1VF5.Q explicitly.

These chains are represented by chain 4OGQ.D which has more than 70% sequence identity.

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

 
 
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To see how chain 1VF5.Q compares with the representative chain PDP:4OGQDa select a method below:





Entity #5: Chains: E,R
Description: PROTEIN PET L protein
Length: 32
No structure alignment results are available for 1VF5.E, 1VF5.R explicitly.

These chains are represented by chain 4PV1.E which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4PV1.E

 
 
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To see how chain 1VF5.R compares with the representative chain PDP:4PV1E_ select a method below:





Entity #6: Chains: F,S
Description: PROTEIN PET M protein
Length: 35
No structure alignment results are available for 1VF5.F, 1VF5.S explicitly.

These chains are represented by chain 4OGQ.F which has more than 70% sequence identity.

 Click here to show the structure comparison results for representative 4OGQ.F

 
 
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To see how chain 1VF5.S compares with the representative chain PDP:4OGQF_ select a method below:





Entity #7: Chains: G,T
Description: PROTEIN PET G protein
Length: 37
No structure alignment results are available for 1VF5.G, 1VF5.T explicitly.

These chains are represented by chain 4OGQ.G which has more than 70% sequence identity.

 Click here to show the structure comparison results for representative 4OGQ.G

 
 
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To see how chain 1VF5.T compares with the representative chain PDP:4OGQGa select a method below:





Entity #8: Chains: H,U
Description: PROTEIN PET N protein
Length: 29
No structure alignment results are available for 1VF5.H, 1VF5.U explicitly.

These chains are represented by chain 4OGQ.H which has more than 70% sequence identity.

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

 
 
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To see how chain 1VF5.U compares with the representative chain PDP:4OGQH_ select a method below:





  • Update Status Hide
    Dec 02 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

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Documentation

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