POP-OUT | CLOSE
 

Structure Alignment View

Pre-calculated jFATCAT_rigid results for d3bmva4 vs. PDP:3DHUAa .
 

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

Structure Alignment Results
Alignment Details: Query: (
 
orange/dark grey)
Cyclomaltodextrin glucanotransferase3bmv A:1-406 c.1.8.1 (Trans)glycosidases
Subject: (
 
cyan/light grey)
Alpha-amylase
P-value: 1.56e-11
Score: 594.12
RMSD: 3.05
%Id: 15.0%
3BMV
PDB ID: 3BMV
SCOP domain d3bmva4
Length: 406
Similarity: 79%
EC number: 2.4.1.19
3DHU
PDB ID: 3DHU
PDP Domain: PDP:3DHUAa
Length: 338
Similarity: 95%
EC number: 3.2.1.1
 
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 d3bmva4 or PDP:3DHUAa
 
 
Jmol
Tip: right-mouse click on Jmol to get access to additional Jmol functionality.
Display Query & Target Style Color
Toggle Selection H-Bonds SS Bonds Rotation Antialias Display (nicer) Black Background
Color Legend
 
d3bmva4 |
 
PDP:3DHUAa
 
 
 

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

 
 
Download Alignment
 
 
Help

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 jFATCAT_rigid algorithm, a Java port of the original FATCAT algorithm.

Yuzhen Ye & Adam Godzik (2003)
Flexible structure alignment by chaining aligned fragment pairs allowing twists. 
Bioinformatics vol.19 suppl. 2. ii246-ii255.
[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.