Methods 2ece: Difference between revisions

From MDWiki
Jump to navigationJump to search
Line 20: Line 20:




'''Query name''': SBP 1 ( 2ECE )
 
 
[[Image:SABLE.gif|frame|border|left|'''Figure 2''' SBP amino acid structure prediction derived from the SABLE server prediction- '''Query name''': SBP 1 ( 2ECE )
Structure prediction by SABLE
Structure prediction by SABLE


Line 26: Line 28:
'''Data source''': Derived from the SABLE server prediction
'''Data source''': Derived from the SABLE server prediction


]]


[[Image:SABLE.gif|frame|border|left|'''Figure 2''' SBP amino acid structure prediction derived from the SABLE server prediction
]]





Revision as of 06:45, 9 June 2008

STRUCTURAL ANALYSIS

SBP 1 Amino Acid FASTA FORMAT Sequence

>2ECE:A|PDBID|CHAIN|SEQUENCE

MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP

abc


Figure 1 X-ray structure of hypothetical selenium-binding protein from Sulfolobus tokodaii, ST0059 ( http://www.proteopedia.org/wiki/index.php/2ece ) and the JenaLib Jmol viewer showing SBP 1 secondary structure spinning [http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2ece&MODE=asymmetric




Figure 2 SBP amino acid structure prediction derived from the SABLE server prediction- Query name: SBP 1 ( 2ECE ) Structure prediction by SABLE Data source: Derived from the SABLE server prediction



WARNING! Given sequence appeared to be a soluble protein, no TM domains found!

Output format is the following:

1st line -> residue numeration

2nd line -> query amino acid sequence

3rd line -> trans-membrane domain prediction (T-TM region, N-soluble part)

     MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKI
    NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                                           
     VHKVELPYINDELHHFGWNACSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREP
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                                             
     KIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEGEGPGGILMLDHYSFEPLGKW
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                                      
     EIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                                       
     IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEI
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                                      
     PAEPLEGNLPEILKPFKAVPPLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTG
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                                     
     KVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNSLYSTWDNQFYPEGLKGWMVK
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                                  
     LNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP
     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Figure 3 SABLE server results.



Movie0001.png

Figure 4 Shows structural helices(red) and beta sheets (yellow) of SBP designed from pymol


Secondary structure.gif

Figure 5


Pdb cartoon 2ece.png

Figure 6

STRUCTURAL COMPARISONS

Surface of 2ece.png

Surface Structure of SBP: Note the few clefts compared to the DNA isomerase shown below.


1YUA SURFACE STRUCTURE.JPG]]]

[1]

Rat fatty acid binding protein 2IFB.jpg

Rat fatty acid binding protein 2IFB, a was found to have 92.5% homology to 14 KDa Selenium binding protein purified from rat liver using column chromatography and SDS-Gel techniques.([ref 3])



Explore SBP features and structural summary here [2].The domains of SBP are shown here [3] Notice how the domains are similar to the putative Isomerase domains of E.coli below.


1RI6 DOMAINS


1RI6 A 0.png


1RI6 A 1.png


1RI6 A 2.png


1RI6 A 3.png


2ECE DOMAINS


2ece A 3.png


2ece A 2.png


2ece A 1.png


2ece A 0.png








Ligand of bovine.png


(Complex Of Bovine Odorant Binding Protein (Obp) With A Selenium Containing Odorant)"Image:Ligand of bovine.png" [[4]]

SEQUENCE ANALYSIS

Selenium binding protein 1 (SELENBP1) SELECTED PROTEIN SIMILARITIES Comparison of sequences in UniGene with selected protein reference sequences. The alignments can suggest function of a gene. [5]