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An Information Portal to 105339 Biological Macromolecular Structures

 

Structure Alignment View

Pre-calculated jCE Circular Permutation results for 1VHR.A vs. 2IHB.A .
 

This page provides a summary view of the protein structure alignment.

Structure Alignment Results
Alignment Details: Query: (
 
orange/dark grey)
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
Subject: (
 
cyan/light grey)
Guanine nucleotide-binding protein G(k) subunit alpha
Z-score: 3.29
Score: 376.17
RMSD: 4.72
%Id: 7.6%
1VHR
PDB ID: 1VHR
Chain ID: A
Length: 178
Similarity: 72%
EC number(s): 3.1.3.16
3.1.3.48
2IHB
PDB ID: 2IHB
Chain ID: A
Length: 317
Similarity: 40%
EC number:
 
Comparison Method
Select these two chains for other comparison:
Click here to align other protein chains. Back to the all vs. all search results for 1VHR.A or 2IHB.A
 
 
Jmol
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Color Legend
Show All Blocks
Block 1
 
1VHR.A |
 
2IHB.A
Block 2
 
1VHR.A |
 
2IHB.A
 
 
 

It is also possible to view this alignment using the stand-alone Java Web Start application.

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

Algorithm: The alignment displayed on this page is based on the jCE Circular Permutation algorithm, a Java port of the original Combinatorial Extension (CE) algorithm. (Implementation by Spencer Bliven and Andreas Prlić).

I.N. Shindyalov, P.E. Bourne (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. 
Protein Eng 11: 739-747
[pdf  ]

RCSB PDB Comparison Tool Reference
Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
Pre-calculated protein structure alignments at the RCSB PDB website
Bioinformatics 26: 2983-2985
[PubMed]

For more information on the algorithms see here.