Starter project · Beginner
Read your first protein structure
Inspect the experimental crambin structure 1CRN and turn its metadata and residue information into a short scientific report.
The question
What does this experimental structure show, and what evidence should accompany a structural interpretation?
Before you begin: Basic Python and protein biology.
The data
RCSB PDB entry 1CRN, downloaded as mmCIF by the supplied script. The entry is an experimental structure, not an AlphaFold prediction.
What you’ll make
- A downloaded mmCIF file and a residue summary table
- A report of experimental method, resolution, chains, and residue counts
- An interpretation exercise linking structure to validation information
Work through it
- Run the supplied script, open the structure in a molecular viewer, and identify chains and secondary structure.
- Read the entry's experimental and validation information before describing its quality.
- Explain what the residue B-factors represent in this experimental context.
- For a later extension, choose a matched experimental/predicted protein pair and assess sequence correspondence and prediction confidence.
Read alongside the project
- PDB-101: understanding PDB data ↗
A welcoming introduction to structure files, experimental information, assemblies, and interpretation.
Guide · Beginner · Free · English - Biopython Tutorial and Cookbook ↗
Practical biological sequence and structure handling, including parsers used in the protein-structure starter project.
Documentation · Intermediate · Free · English - UCSF ChimeraX tutorials ↗
Learn molecular visualization through worked examples; check the current software license for your intended use.
Tutorial · Beginner · Tutorials free; software terms vary by use · English - Interpreting AlphaFold confidence scores ↗
Understand local confidence and relative-domain uncertainty before using a prediction to support a biological claim.
Guide · Intermediate · Free · English