Introduction to structural biology
Uniprot
Uniprot: https://www.uniprot.org/Text search
- Access Uniprot
- Enter LinB Sphingomonas paucimobilis in the search bar.
- Select the first entry.
- Examine the entry:
- Explore the “Function” section for information on the enzyme’s role
- Find the UniProt ID and Accession Number
- Review the protein name, organism, and gene name
- Structure information
- Scroll to the "Structure" section
- Find the entry with the lowest resolution.
- Click on the PDB link to view the 3D structure.
- Catalytic residues
- Identify the catalytic triad
- Which amino acid acts as a nucleophile in the reaction?
PDB Database
RCSB PDB: https://www.rcsb.org/Text search
- Access the PDB Database.
- Search for the structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis in the RCSB PDB database.
- How many records did you find?
Advanced search
- Search for haloalkane dehalogenase LinB structures from the organism Sphingomonas paucimobilis with a bound ligand.
- How many LinB-ligand complexes did you find?
- Give an example of several ligands
- find and state the PDB-ID code of the free form LinB (ligand-free structure)
Results report
- Return to the results of the searched LinB-ligand complexes and prepare a result report containing, among other things, information on resolution, ligands, and release date of individual structures
- Which LinB structure has the highest resolution?
- Which LinB structure with bound ligand 1,3-propanediol was released in the database first?
- Access the PyMOL home page.
- Click on “DOWNLOAD NOW” link.
- Select the installer suitable for your operating system.
- Continue with the download and installation.
- Obtaining license:
- Option 1:
- You can download an educational license provided (check MUNI Google Workspace)
- Option 2:
- You can also apply for an educational license
- Click “BUY LICENCE“ on the home page
- Click on “Student/Teacher”
- Enter your information together with your academic mail address.
- You’ll receive a download link with a username and password shortly.
- You can also apply for an educational license
- You can continue to use PyMol without a license for 30 days without any warnings.
Visualization
- Basic handling
- Visualization Types
- Coloring
- Preset Styles
Working with selections
- Selection from the structure
- Selection from the sequence
- Selection by command: sele (help select, help selection)
- Modify selection
Analysis
- Measurement
- Polar contacts
Preparing Images
- Structure Modification
- Transparency and color settings
- Saving the image and project
- Scene saving
- Option 1: