ProteinStructure/about.md

ProteinStructure — Test Entries

Species-independent 3D protein structures, organized by PDB ID. Each entry directory contains the same structure in two formats:

• <PDB_ID>.pdb — legacy PDB format (fixed-column text)
• <PDB_ID>.cif — mmCIF format (preferred for modern tooling and large complexes)

Both files describe the same atomic coordinates; choose by tool compatibility.

Available Entries

PDB ID	Source Organism	Molecule	Method	Notes
1AKI	Gallus gallus (chicken)	Hen egg-white lysozyme	X-ray diffraction, 1.5 Å	Classic small enzyme; widely used in MD tutorials (e.g., GROMACS lysozyme tutorial).
1CRN	Crambe hispanica subsp. abyssinica	Crambin	X-ray diffraction	Very small (46 residues); fast to parse, good smoke-test entry.

Suggested Uses

• Structure parsing (Bio.PDB, gemmi, MDAnalysis)
• Format conversion (PDB ↔ mmCIF)
• Visualization (PyMOL, ChimeraX, NGLview)
• Secondary-structure assignment (DSSP), surface/pocket analysis
• Lightweight inputs for molecular dynamics setup demos

Notes

These entries are not linked to the reference genomes under SaccharomycesCerevisiae/ or StaphylococcusAureus/. They are keyed by PDB ID, not by species.

Source: RCSB PDB (https://www.rcsb.org/).