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Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222
3IDX

Structural Similarities for the Entities in PDB 3IDX

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: G
Description: HIV-1 HxBc2 gp120 core protein
Length: 317
No structure alignment results are available for 3IDX.G explicitly.

It is represented by chain 2NXY.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 2NXY.A

 
 
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To see how chain 3IDX.G compares with the representative chain d2nxya1 select a method below:





Entity #2: Chains: H
Description: Fab b13 heavy chain protein
Length: 231
No structure alignment results are available for 3IDX.H explicitly.

It is represented by chain 4NZU.L which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 4NZU.L

 
 
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To see how chain 3IDX.H compares with the representative chain PDP:4NZULa select a method below:





Entity #3: Chains: L
Description: Fab b13 light chain protein
Length: 215
No structure alignment results are available for 3IDX.L explicitly.

It is represented by chain 4NZU.L which has more than 90% sequence identity.

 Click here to show the structure comparison results for representative 4NZU.L

 
 
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To see how chain 3IDX.L compares with the representative chain PDP:4NZULa select a method below:





  • Update Status Hide
    Oct 21 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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PDB 1: Chain 1: ...
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Documentation

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