1. Data retrieval

• Go to PDB mirror site at National Tsing Hua University
• http://pdb.life.nthu.edu.tw/
• Go to Protein Data Bank
• Go to SearchLite
• Type in " transcription regulation " -> Search
• Your query found 185 structures
• Go to Pull down to select option:
• Select " Refine Your Query " -> Go
• Type in " technique: x-ray " -> Search
• Go to Pull down to select option:
• Select " Refine Your Query " -> Go
• Type in " source: saccharomyces " -> Search
• Your query found 9 structures
• Select 1D66. Go to {EXPLORE}

2. View Structure         

• Interactive 3D Display
• Rasmol
• FirstGlance (needs Chime)
• Still Images:
•  Ribbons (250x250)  Cylinders (250x250)
•  Ribbons (500x500)  Cylinders (500x500)
• Custom Size Images:
• Size : Type " 800 "
• Format: Choose " JPEG "
• Creat Image

3. Download/Display File

• Display the Structure File:
• complete with coordinates
• "header only" (no coordinates)
• Download the Structure File:
• noncompressed file
• compressed file

4. Structural Neighbors

• CATH - Class, Architecture, Topology and Homologous superfamily
• CE - Combinatorial Extension of the optimal path
• FSSP - Fold classification based on Structure-Structure alignment of Proteins
• SCOP - Structural Classification Of Proteins
• VAST - Vector Alignment Search Tool

5. Geometry

• Dihedral Angles
• Common Bond Angles
• Bond Lengths

6. Other Sources

• Sequence Data - 14 links
• Structure Data - 55 links
• Motifs and Domains - 13 links
• Analysis - 50 links
• Visualization - 23 links
• Literature - 3 links
• Miscellaneous - 20 links

7. Sequence Details

8. Crystallization Info

9. NDB Atlas Entry

10. Quick Report

 

 

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                                                                                                                                                 PCL