Structural analysis of 2qgn

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Protein Sequence in FASTA format

>gi|152149497|pdb|2QGN|A Chain A, Crystal Structure Of Trna Isopentenylpyrophosphate Transferase (Bh2366) From Bacillus Halodurans, Northeast Structural Genomics Consortium Target Bhr41. XKEKLVAIVGPTAVGKTKTSVXLAKRLNGEVISGDSXQVYRGXDIGTAKITAEEXDGVPHHLIDIKDPSE SFSVADFQDLATPLITEIHERGRLPFLVGGTGLYVNAVIHQFNLGDIRADEDYRHELEAFVNSYGVQALH DKLSKIDPKAAAAIHPNNYRRVIRALEIIKLTGKTVTEQARHEEETPSPYNLVXIGLTXERDVLYDRINR RVDQXVEEGLIDEAKKLYDRGIRDCQSVQAIGYKEXYDYLDGNVTLEEAIDTLKRNSRRYAKRQLTWFRN KANVTWFDXTDVDFDKKIXEIHNFIAGKLEEKSKLEHHHHHH

Structure of Protein

Figure 1
Structure of TRNA isopentenyl transferase 1 showing helix, sheet and loop. Image constructed from PyMOL.


Secondary Structure

Analysis of the secondary structure acquired from Protein Data Bank showed results as displayed below :

Secondary.jpg

Surface Properties of 2qgn

Figure 2
Surface property displayed by 2qgn. Red colour indicates negatively charged regions, while blue colour indicates positively charged regions.


Domains

There are two main domains regarding 2qgnA.

Figure 4
Two main domains exhibited by tRNA isopentenyl transferase(2qgnA). Blue regions denote one domain while Red regions underlying another domain.


Domain--2.jpg Domain--1.jpg


Ligand Binding Sites and Surface Clefts

Ligand.png
Surface cleft.png

Structural Alignment

Dali Output

PDB entry code for 2qgn was loaded onto DALI to search for structurally similar neighbours. Displayed below are the results from DALI search :-

Dali output.jpg

A total of 527 hits were found from DALI search, thus only the first 20 hits that may be of significance were shown on the figure. Based on the outcome of DALI, PDB files of each structurally similar protein was obtained from PDB. These were each superimposed with 2qgn on PyMOL, to compare the structural similiarity. Results are as below :

2qgn.png
2qgn2.png
2qgn421.jpg