| id | Class | Fold | Superfamily | Family |
|---|
| 1.27.1.1 | All alpha proteins | 4-helical cytokines | 4-helical cytokines | Long-chain cytokines |
| 1.27.1.2 | All alpha proteins | 4-helical cytokines | 4-helical cytokines | Short-chain cytokines |
| 1.36.1.2 | All alpha proteins | lambda repressor-like DNA-binding domains | lambda repressor-like DNA-binding domains | Phage repressors |
| 1.36.1.5 | All alpha proteins | lambda repressor-like DNA-binding domains | lambda repressor-like DNA-binding domains | Bacterial repressors |
| 1.4.1.1 | All alpha proteins | DNA/RNA-binding 3-helical bundle | Homeodomain-like | Homeodomain |
| 1.4.1.2 | All alpha proteins | DNA/RNA-binding 3-helical bundle | Homeodomain-like | Recombinase DNA-binding domain |
| 1.4.1.3 | All alpha proteins | DNA/RNA-binding 3-helical bundle | Homeodomain-like | Myb |
| 1.41.1.2 | All alpha proteins | EF Hand-like | EF-hand | S100 proteins |
| 1.41.1.5 | All alpha proteins | EF Hand-like | EF-hand | Calmodulin-like |
| 1.45.1.2 | All alpha proteins | Met repressor-like | Met repressor-like | Bacterial repressors |
| 2.1.1.1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | V set domains (antibody variable domain-like) |
| 2.1.1.2 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | C1 set domains (antibody constant domain-like) |
| 2.1.1.3 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | C2 set domains |
| 2.1.1.4 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | I set domains |
| 2.1.1.5 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | E set domains |
| 2.28.1.1 | All beta proteins | ConA-like lectins/glucanases | ConA-like lectins/glucanases | Legume lectins |
| 2.28.1.3 | All beta proteins | ConA-like lectins/glucanases | ConA-like lectins/glucanases | Galectin (animal S-lectin) |
| 2.38.4.1 | All beta proteins | OB-fold | Nucleic acid-binding proteins | Anticodon-binding domain |
| 2.38.4.3 | All beta proteins | OB-fold | Nucleic acid-binding proteins | Single strand DNA-binding domain, SSB |
| 2.38.4.5 | All beta proteins | OB-fold | Nucleic acid-binding proteins | Cold shock DNA-binding domain-like |
| 2.44.1.2 | All beta proteins | Trypsin-like serine proteases | Trypsin-like serine proteases | Eukaryotic proteases |
| 2.5.1.1 | All beta proteins | Cupredoxins | Cupredoxins | Plastocyanin/azurin-like |
| 2.5.1.3 | All beta proteins | Cupredoxins | Cupredoxins | Multidomain cupredoxins |
| 2.52.1.2 | All beta proteins | PH domain-like | PH domain-like | Phosphotyrosine-binding domain (PTB) |
| 2.56.1.2 | All beta proteins | Lipocalins | Lipocalins | Fatty acid binding protein-like |
| 2.9.1.2 | All beta proteins | Viral coat and capsid proteins | Viral coat and capsid proteins | Plant virus proteins |
| 2.9.1.3 | All beta proteins | Viral coat and capsid proteins | Viral coat and capsid proteins | Insect virus proteins |
| 2.9.1.4 | All beta proteins | Viral coat and capsid proteins | Viral coat and capsid proteins | Animal virus proteins |
| 3.1.8.1 | Alpha and beta proteins (a/b) | TIM beta/alpha-barrel | Glycosyltransferases | alpha-Amylases, N-terminal domain |
| 3.1.8.3 | Alpha and beta proteins (a/b) | TIM beta/alpha-barrel | Glycosyltransferases | beta-glycanases |
| 3.2.1.2 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | Tyrosine-dependent oxidoreductases |
| 3.2.1.3 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain |
| 3.2.1.4 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | Formate/glycerate dehydrogenases, NAD-domain |
| 3.2.1.5 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | Lactate & malate dehydrogenases, N-terminal domain |
| 3.2.1.6 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase-like, N-terminal domain |
| 3.2.1.7 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | Amino-acid dehydrogenase-like, C-terminal domain |
| 3.3.1.2 | Alpha and beta proteins (a/b) | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | FAD-linked reductases, N-terminal domain |
| 3.3.1.5 | Alpha and beta proteins (a/b) | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, N-terminal and central domains |
| 3.32.1.1 | Alpha and beta proteins (a/b) | P-loop containing nucleotide triphosphate hydrolases | P-loop containing nucleotide triphosphate hydrolases | Nucleotide and nucleoside kinases |
| 3.32.1.11 | Alpha and beta proteins (a/b) | P-loop containing nucleotide triphosphate hydrolases | P-loop containing nucleotide triphosphate hydrolases | RecA protein-like (ATPase-domain) |
| 3.32.1.13 | Alpha and beta proteins (a/b) | P-loop containing nucleotide triphosphate hydrolases | P-loop containing nucleotide triphosphate hydrolases | Extended AAA-ATPase domain |
| 3.32.1.8 | Alpha and beta proteins (a/b) | P-loop containing nucleotide triphosphate hydrolases | P-loop containing nucleotide triphosphate hydrolases | G proteins |
| 3.42.1.1 | Alpha and beta proteins (a/b) | Thioredoxin fold | Thioredoxin-like | Thioltransferase |
| 3.42.1.5 | Alpha and beta proteins (a/b) | Thioredoxin fold | Thioredoxin-like | Glutathione S-transferases, N-terminal domain |
| 3.42.1.8 | Alpha and beta proteins (a/b) | Thioredoxin fold | Thioredoxin-like | Glutathione peroxidase-like |
| 7.3.10.1 | Small proteins | Knottins (small inhibitors, toxins, lectins) | EGF/Laminin | EGF-type module |
| 7.3.5.2 | Small proteins | Knottins (small inhibitors, toxins, lectins) | omega toxin-like | Spider toxins |
| 7.3.6.1 | Small proteins | Knottins (small inhibitors, toxins, lectins) | Scorpion toxin-like | Long-chain scorpion toxins |
| 7.3.6.2 | Small proteins | Knottins (small inhibitors, toxins, lectins) | Scorpion toxin-like | Short-chain scorpion toxins |
| 7.3.6.4 | Small proteins | Knottins (small inhibitors, toxins, lectins) | Scorpion toxin-like | Plant defensins |
| 7.39.1.2 | Small proteins | Glucocorticoid receptor-like (DNA-binding domain) | Glucocorticoid receptor-like (DNA-binding domain) | Nuclear receptor |
| 7.39.1.3 | Small proteins | Glucocorticoid receptor-like (DNA-binding domain) | Glucocorticoid receptor-like (DNA-binding domain) | LIM domain |
| 7.41.5.1 | Small proteins | Rubredoxin-like | Rubredoxin-like | Rubredoxin |
| 7.41.5.2 | Small proteins | Rubredoxin-like | Rubredoxin-like | Desulforedoxin |