Below are some molecules that demonstrate the range
of capabilities in FirstGlance in Jmol.
Clicking on one of the
four character PDB identification codes
below will display that molecule in FirstGlance.
FirstGlance will obtain these published examples from the World Wide Protein
Data Bank (rcsb.org).
- 6ZGG: Primed spike protein of SARS-CoV-2 (COVID-19 virus). See Priming, Mutations, and Fusion Transformation.
- 2CYH: Cyclophilin A complexed with dipeptide Ala-Pro. Four terminal charges.
- 1D66: Gal 4 (transcriptional regulatory protein) DNA-binding domain complexed with DNA double helix. Cd ions.
- 1IJW: Hin recombinase recognizing DNA double helix.
Protein, DNA, multiple ligands, non-standard residues, missing residues, incomplete sidechains, alternate locations.
- 2HHD: Hemoglobin (deoxy) tetramer with heme, water, sulfate.
Chain A has all five categories of non-covalent bonds in its Contacts...
- 1BL8: Potassium channel with K+.
Use Hydrophobic/Polar to see the lipophilic surface. Find.. TRP while viewing Vines.. (sidechains hidden) to see the dimensions of the lipid bilayer.
- 1PGB: Staph Protein G (small protein with both alpha and beta secondary structures), water.
- 3HYD: Peptide (7 amino acids), high resolution (1.0 Å) with hydrogen and alternate locations.
- 1ABT: Alpha-bungarotoxin complexed with receptor peptide. Five disulfide bonds. NMR, 4 models. All hydrogens present (no water).
- 1IGT: Immunoglobulin G2a. 12 intrachain and 3 interchain disulfides. Glycosylation. Some hydrogens modeled in (no water).
- 1BKX: C kinase. Phosphoserine (SEP) and phosphothreonine (TPO) display as non-standard residues.
Some water. Contains an isolated single nucleotide ligand.
- 1APM: C kinase with peptide inhibitor and N-octane (OCT), water. Phosphorylated serine (SEP) and threonine (TPO) are marked non-standard residues. Has many incomplete sidechains: Try Charge...
- 4CPA: Carboxypeptidase A with Zn++. No water. Contains an isolated single amino acid ligand and GLX (use Find..).
- 104D: Synthetic DNA/RNA hybrid. No water.
- 1EVV: tRNA including many non-standard nucleotides and water. 5' terminus is phosphorylated (view with Tools, Ends).
- 1LCD: Lac repressor DNA binding domain, bound to DNA double helix. NMR, 3 models. Water has hydrogens.
- 3GCA: Riboswitch (transcriptional regulator) RNA aptamer domain bound to a modified guanine precursor necessary for tRNA wobbling (Spitale et al., 2009).
- 2BBN: Calmodulin with Ca++ and bound peptide. NMR, 21 models.
- 3IF7: Calmodulin with Ca++ and large ligand.
- 5MCT: DNA recognition by p53.
The asymmetric unit has only half of the DNA double helix.
Biological Unit 1 has 2 copies of the asymmetric unit, forming the double helix.
- 1K28: Bacterial cell wall puncturing device of bacteriophage T4.
The asymmetric unit would not be a stable protein by itself.
Biological Unit 1 has 3 copies of the asymmetric unit.
Selenomethionines (MSE) display as non-standard residues.
The following examples are not available from the Protein Data Bank.
FirstGlance will obtain them from other servers.
- bilagram.pdb.gz: Theoretical model of lipid bilayer with gramicidin channel. Model distributed with permission of Serge Crouzy, on the condition that any derivative work must explicitly cite Crouzy, S., T. B. Woolf and B. Roux, Biophys. J. 67:1370-86, 1994.
ConSurf Examples: (Generated by the ConSurf Server)
These PDB files were pre-processed by the ConSurf Server,
so they contian ConSurf results in their headers.
See also
Exploring ConSurf Results
in FirstGlance in Jmol.
Additional ConSurf results (including for AlphaFold predictions) are in
Versions. Use your browser's Edit/Find to locate the word consurf.
Enolase, an enzyme in glycolysis:
Major Histocompatibility Class I with bound viral peptide:
Thrombin complexed with fibrinopeptide.
Flp recombinase complexed with DNA Holliday junction.
PDB files with lower case chain names. See Jmol/Visualizing Large Molecules: 62 Chain Limit
- 3jqo_consurf-apd1.1.pdb.gz: 42 chains. ConSurf processed chain "b", which is sequence-identical with chains ADGJMPSVYehkn (14 chains including "b"). Type IV secretion system outer membrane complex.
- 7o3e_consurf-apd1.03.pdb.gz: 31 chains. ConSurf processed unique chain "a", which contains a His-Tyr crosslink. (Mitochondrial supercomplex.)
More molecules:
To browse PDB codes for other interesting molecules, please go to the
Atlas
of Macromolecules or
Molecule of the Month
or the
Table of Contents of Proteopedia,
or
search the
Protein Data Bank.
Feedback to
the FirstGlance Development Team.
