From http://www.rcsb.org/pdb/101/motm_archive.do

1. AAA+ proteases
2. Acetylcholine receptor
3. Acetylcholinesterase
4. Aconitase and iron regulatory protein 1
5. Actin
6. Adenovirus
7. Adrenergic receptors
8. Alcohol dehydrogenase
9. Alpha-amylase
10. Aminoacyl-tRNA synthetases
11. Aminoglycoside antibiotics
12. Amyloid-beta precursor protein
13. Anabolic steroids
14. Anthrax toxin
15. Antibodies
16. Antifreeze proteins
17. ATP synthase
18. Auxin and TIR1 ubiquitin ligase
19. Bacteriophage phiX174
20. Bacteriorhodopsin
21. Beta-secretase
22. Cadherin
23. Calcium pump
24. Calmodulin
25. cAMP-dependent protein kinase (PKA)
26. Carbonic anhydrase
27. Carotenoid oxygenase
28. Caspases
29. Catabolite activator protein
30. Catalase
31. Chaperones
32. Cholera toxin
33. Circadian clock proteins
34. Citrate synthase
35. Clathrin
36. Collagen
37. Complex I
38. Concanavalin A and circular permutation
39. Crystallins
40. Cyclooxygenase
41. Cytochrome bc1
42. Cytochrome c oxidase
43. Cytochrome c
44. Cytochrome p450
45. Dengue virus
46. Designed DNA crystal
47. Designer proteins
48. Dihydrofolate reductase
49. DNA ligase
50. DNA methyltransferases
51. DNA polymerase
52. DNA
53. Elongation factors
54. Enhanceosome
55. Epidermal growth factor
56. Estrogen receptor
57. Exosomes
58. Fatty acid synthase
59. Ferritin and transferrin
60. Fibrin
61. G proteins
62. Glucansucrase
63. Glucose oxidase
64. Glutamine synthetase
65. Glycogen phosphorylase
66. Glycolytic enzymes
67. Green fluorescent protein (GFP)
68. Growth hormone
69. Hemagglutinin
70. Hemoglobin
71. HIV-1 protease
72. Hsp90
73. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
74. Importins
75. Influenza neuraminidase
76. Insulin
77. Integrase
78. Integrin
79. Inteins
80. Interferons
81. Isocitrate dehydrogenase
82. Kinesin
83. lac repressor
84. Lactate dehydrogenase
85. Leptin
86. Luciferase
87. Lysozyme
88. Major histocompatibility complex
89. Mechanosensitive channels
90. Messenger RNA capping
91. Multidrug resistance transporters
92. Myoglobin
93. Myosin
94. Nanobodies
95. Neurotrophins
96. Nitric oxide synthase
97. Nucleosome
98. O-GlcNAc transferase
99. Oct and Sox transcription factors
100. Oxidosqualene cyclase
101. P-glycoprotein
102. p53 tumor suppressor
103. Parvoviruses
104. PDB pioneers prefer PDB
105. Penicillin-binding proteins
106. Pepsin
107. Photosystem I
108. Photosystem II
109. Poliovirus and rhinovirus
110. Poly(A) polymerase
111. Potassium channels
112. Prions
113. Pyruvate dehydrogenase complex
114. Ras protein
115. Restriction enzymes
116. Reverse transcriptase
117. Rhodopsin
118. Rhomboid protease GlpG
119. Ribonuclease A
120. Ribosomal subunits
121. Ribosome
122. Riboswitches
123. RNA polymerase
124. Rubisco
125. Selenocysteine synthase
126. Self-splicing RNA
127. Serpins
128. Serum albumin
129. Simian virus 40
130. Sliding clamps
131. Small interfering RNA (siRNA)
132. Sodium-potassium pump
133. Src tyrosine kinase
134. Sulfotransferases
135. Superoxide dismutase
136. T-cell receptor
137. TATA-binding protein
138. Thrombin
139. Thymine dimers
140. Tissue factor
141. Tobacco mosaic virus
142. Toll-like receptors
143. Topoisomerases
144. Transfer RNA
145. Transposase
146. Trypsin
147. Ubiquitin
148. Vaults
149. Vacuolar ATPase
150. Xanthine oxidoreductase
151. Zinc fingers