| Complex | Proteins |
| 20 2-oxoglutarate dehydrogenase | 3 |
| 40 Alpha-agglutinin anchor | 2 |
| 60 Anaphase promoting complex (APC) | 11 |
| 70 Anthranilate synthase | 2 |
| 75 Arginase | 1 |
| 80 Arginine-specific carbamoylphosphate synthase | 2 |
| 90 Assembly complexes | 7 |
| 100 Calcineurin B | 3 |
| 110 cAMP-dependent protein kinase | 4 |
| 120 Casein kinase | 8 |
| 123 Catalase | 2 |
| 125 Cell cycle checkpoint complexes | 2 |
| 130 Chaperonine containing T-complex TRiC (TCP RING Complex) | 8 |
| 132 CTP synthetase | 1 |
| 133 Cyclin-CDK (Cyclin-dependent kinases) complexes | 25 |
| 140 Cytoskeleton | 73 |
| 143 D-arabinose dehydrogenase | 1 |
| 145 delta3-cis-delta2-trans-enoyl-CoA isomerase | 1 |
| 150 Endonuclease SceI, mitochondrial | 1 |
| 160 Exocyst complex | 7 |
| 170 Fatty acid synthetase, cytoplasmic | 2 |
| 172 Fatty acid synthetase, mitochondrial | 1 |
| 177 Gim complexes | 5 |
| 180 Prenyltransferases | 6 |
| 190 Glucan synthases | 5 |
| 200 Glycine decarboxylase | 4 |
| 210 H+-ATPase, plasma mebrane | 4 |
| 220 H+-transporting ATPase, vacuolar | 15 |
| 225 Hexokinase 2 | 1 |
| 230 Histone acetyltransferase complexes | 19 |
| 240 Histone deacetylase complexes | 5 |
| 250 Isocitrate dehydrogenase | 2 |
| 253 Isocitrate lyase | 1 |
| 260 Intracellular transport complexes | 95 |
| 265 Kel1p/Kel2p complex | 2 |
| 270 Kinetochore protein complexes | 28 |
| 280 L-aminopadipate-semialdehyde dehydrogenase | 2 |
| 290 Mitochondrial translocase complex | 18 |
| 295 Nem1p-Spo7p complex | 2 |
| 300 Nonsense-mediated mRNA decay pathway complex | 3 |
| 310 Nuclear pore complex (NPC) | 24 |
| 320 Nucleosomal protein complex | 8 |
| 325 Ornithine carbamoyltransferase | 1 |
| 330 Phenylalaninine-tRNA-ligase | 3 |
| 340 Phosphofructokinase | 2 |
| 350 Proteases, mitochondrial | 8 |
| 360 Proteasome | 36 |
| 370 Protein N-acetyltransferase | 2 |
| 390 Pyruvate dehydrogenase | 5 |
| 380 Pyruvate kinase | 2 |
| 400 RSC complex (Remodel the structure of chromatin) | 10 |
| 410 Replication complexes | 55 |
| 420 Respiration chain complexes | 56 |
| 430 Ribonucleoside-diphosphate reductase | 4 |
| 440 RNA processing complexes | 129 |
| 443 S-adenosyl-methionine delta-24-sterol-c-methyltransferase | 1 |
| 445 SCF (Skp1-Cdc53-F-box protein) comlexes | 7 |
| 450 Serine/threonine phoshpoprotein phosphatase | 6 |
| 470 Signal transduction complexes | 16 |
| 475 Nuclear cohesion | 9 |
| 480 Spindle pole body (SPB) | 32 |
| 485 Succinyl-CoA ligase | 2 |
| 490 Synaptonemal complex (SC) | 5 |
| 500 Translation complexes | 266 |
| 510 Transcription complexes/Transcriptosome | 195 |
| 520 Translocon | 29 |
| 550 Complexes by Systematic Analysis | 2871 |
| X Proteins assigned to complexes | 2733 |
| - Proteins not assigned | 3273 |
