First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
Topic pages are pages about proteins or molecules or families of proteins or molecules, or structural biology concepts or terms. Topic pages are not titled with a PDB code. In contrast to topic pages, Proteopedia contains a page for each entry in the PDB, created automatically, and titled with the PDB code. These pages generally describe a particular solved structure. A topic page like hemoglobin, however, will address the protein in general, and refer to several solved structures such as 1gzx and 2hbs. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. Also, they are created manually, never automatically.
You might also be interested in Proteopedia's Table of Contents.
means that the article first became available in Proteopedia within the past four months, or that substantial new content was added within the past four months. See also What's New?.
Pages About Molecules (Not Titled with a PDB Code)
The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of all pages whose titles do not begin with a numeral, and here is a list of all pages.
See also: About Macromolecular Structure, a list of pages not listed below.
- AChE inhibitors and substrates, PartII, PartIII
- β2-Adrenergic Receptor, A Physical Model of the
- Amino Acids with info about Selenocysteine and Pyrrolysine
- Antizyme Inhibitor
- ATP Phosphoribosyl Transferase
- Avian Influenza Neuraminidase, Tamiflu and Relenza
B - C
- Bacterial Intein-Like Domains (BILs)
- Believe It or Not!
- Biotin Protein Ligase
- C-di-GMP signaling
D - F
- Dihydrofolate reductase
- Directed evolution
- DNA-binding protein VirE2 (Agrobacterium)
- DnaC helicase loader, structure of (E. coli) (homology model)
- Dinoflagellate luciferase
- Eran Hodis's Favorites
- Eric Martz's Favorites
G - L
- The Glutamate Receptor
- Gramicidin Channel in Lipid Bilayer
- Green Fluorescent Protein
- High school teachers' resources
- Highest impact structures
- Hint auto-proteolytic protein-processing domains
- Intrinsically Disordered Protein
- Ion channels
- Lac repressor
- Lactose Permease
- Large Ribosomal Subunit
- Lipase lid morph
M - N
- Major Histocompatibility Complex Class I: Crucial to your defenses against viruses, and one of the Highest Impact Structures of All Time
- Matrix metalloproteinases
- Mechanosensitive channels: opening and closing (includes morphs)
- Membrane proteins
- Metal-Ligand Polyhedra
- Morphs of conformational changes of macromolecules
- NADH quinone oxidoreductase (NQO1)
- Nitrotyrosine, a post-translational modification occurring in inflammation that often inactivates enzymes.
- Nobel Prizes for 3D Molecular Structure including the 2009 Chemistry Prize for the Ribosome
- Non-Standard Residues, see also Standard Residues
O - P
- PcrA helicase
- Personal favorites
- Photosystem II
- Plant Viral Protein p19 Suppression of RNA Silencing
- Prion protein
- Proton Channels (Includes an animated morph)
- Pyruvate phosphate dikinase
- Recombinase A
- Recoverin, a calcium-activated myristoyl switch
- RecQ-Like protein 1, human
- Reverse transcriptase
- RNA motifs
- Rop protein
- Scene authoring tools
- SelB Recognition
- Serine Protease
- Serine hydrolase
- Serum Paraoxonase
- Sites, Functional
- Standard Residues (see also Non-Standard Residues
- Strictosidine Synthase
- Structures saving the most lives
- Suppression of RNA Silencing by Viruses
T - Z
- TATA-Binding Protein
- Teaching Strategies Using Proteopedia
- TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)
- Tetrameric alcohol dehydrogenases
- Thermal motion of peptide
- Thymidine Kinase, Herpes Simplex Virus
- Transcription Termination Factor Rho
- Treatment of Gaucher disease
- Water with electrostatic potential surface / El Agua
- Zinc Fingers
PDB Code Pages
Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.
- 1d9z The DNA repair protein UVRB in complex with ATP
- 1gm5 Thermotoga maritima RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork.
- 1eve Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.
- 1mr4 Antifungal and insecticidal protein NaD1 from Nicotiana
- 1n4n Defensin from Petunia
- 1ogs Human acid-beta-glucosidase
- 1v04 Paraoxonase-1 via directed evolution
- 1xjo Aminopeptidase
- 2cek Torpedo californica acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.
- 2db3 Drosophila melanogasterDEAD-box helicase protein Vasa.
- 2eyq Escherichia coli Mfd (TRCF, transcription-repair coupling factor).
- 2ic8 Escherichia coli GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family
- 2p18 Leishmania infantum Glyoxalase II
- 2rd0 Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.
- 2rkx Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase
- 2v9d A prophage protein belonging to the dihydrodipicolinic acid synthase family
- 2veo X-ray structure of Candida antarctica lipase A in its closed state
- 3ews Human DExD/H-box RNA-dependent ATPase DDX19 in the open and closed cleft conformation (includes morph).
- 3dmq Escherichia coli Swi2/Snf2 protein RapA that recycles RNA polymerase during transcription.
- 5p21 The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp