Part 1: CATH classification of ubiquitin
For PDB code 1UBI (ubiquitin structure):
• Class: Alpha Beta
• Architecture: Roll
• Topology: Ubiquitin-like (UB roll)
• Homologous superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit
Part 2: SCOPe classification of ubiquitin
For PDB code 1UBI (ubiquitin structure):
• Class: Alpha and beta proteins (a+b)
• Fold: beta-Grasp (ubiquitin-like)
• Superfamily: Ubiquitin-like
• Family: Ubiquitin-related
Part 3: Comparison of two structures in SCOPe
For PDB code 2R2O (effector domain of human Plexin B1):
• Class: Alpha and beta proteins (a+b)
• Fold: beta-Grasp (ubiquitin-like)
• Superfamily: Ubiquitin-like
• Family: Rho GTPase binding domain
Comparison Analysis
• Same Levels: Class, Fold, and Superfamily are identical for both structures.
• Different Levels: They differ at the Family level (Ubiquitin-related vs. Rho GTPase
binding domain).
• Implications: The similarities suggest shared structural features and a probable common
evolutionary origin. The difference at the Family level indicates functional divergence
within the same superfamily.
Part 4: Comparing CATH and SCOPe classification systems
1. Hierarchical organization:
