Structure Protein

From MDWiki
Jump to navigationJump to search

2ifu has 4 chains (A, B, C and D) integrated together to form the whole molecular structure as shown below:

Snap-gamm ligands.png


(chain A= green, chain B= cyan, chain c= purple, and chain d= yellow)

Two molecular components were observed:

sulfate ion (SO4)Sulfate ion.png and selenomethionine (MSE)MSE.png

Ten sulfate ions were observed. Each ion differs in arrangement as well as orientation related with each chains.


protein sequence (FASTA)

>gi|118138356|pdb|2IFU|A Chain A, Crystal Structure Of A Gamma-Snap From Danio Rerio AIAAQKISEAHEHIAKAEKYLKTSFXKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNR SLFHAAKAFEQAGXXLKDLQRXPEAVQYIEKASVXYVENGTPDTAAXALDRAGKLXEPLDLSKAVHLYQQ AAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSXYKEXENYPTCYKKCIAQVLVQLHRAD YVAAQKCVRESYSIPGFSGSEDCAALEDLLQAYDEQDEEQLLRVCRSPLVTYXDNDYAKLAISLKVPGGG GGKKKPSASASAQPQEEEDDEYAGGLC


Strutural analysis

SNAP-GAMMA DALI

Based on Dali search, 6 proteins with highest Z-value were chosen: 1qqe-A (protein transport), 2fi7-A (protein binding), 1a17 (hydrolase), 2ak6-A, 1fch-A (signalling protein), 1haz4-A (transcription factor),

snap-gamma: multiple structure alignment

Snap-gamma: sequence alignment with 1QQE:A


alt text


Dark colors: 2ifu:A Light colors: 1qqe:A

SCOP

multiple alignment results, click here

Structure alignment.png

Superimposed structure between 2ifuA; 2ifuB; 2ifuC; 2ifuD; 1qqeA; and 1b89A


ligand binding domain

Ligandbindingsitepredictioni2.png


electrostatic potential

Electrostatic potential (molecular surface).png

electrostatic potential of proteins mapped into molecular surface. positive potentials are shown in blue while that of negative potential are in red. the electrostatic potential was calculated using Coulomb computational method.

Protein families

has 2 domains: Pfam at Sanger


alignment with:

Pfam-B_7270 (7-66)

highly conserved residue:


Pfam-B_15198 (87-307) highly conserved residue :residue 104, 109, 121, 168

scorecons result indicated a Diversity of position scores: 89.4% where 100%=high diversity


InterProScan Results

2ifuA interpro.png

links

CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17 1QQE

CLATHRIN HEAVY CHAIN PROXIMAL LEG SEGMENT (BOVINE) 1B89

uniprot

http://myhits.isb-sib.ch/cgi-bin/motif_scan

http://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?sdid=181604


http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi

ClustalX-alignment.JPG