Hot answers tagged

17

6405 proteins mapping to 5220 genes, according to Ensembl. In Ensembl's BioMart, you can select the PDB ID as external reference. Export the results and count the unique proteins/genes that have a PDB ID.


13

To make sure I'm not comparing apples and pears, my (attempt to) answer the question will be broken into two parts: comparison of single-stranded nucleic acids and double stranded ones. Single stranded DNA and RNA Both DNA and RNA can form single-stranded complex tertiary structures in which the secondary structure elements are associated through van der ...


10

Ramachandran plots show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions. Dihedral Angles There are limits to possible distributions of phi and psi ...


10

PDB is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins: Open Advanced search tab of the PDB website. Select Biology -> Source organism from the menu. Type Homo sapiens (human). You can reduce redundancy by checking Remove Similar ...


9

The beta-form of DNA and the alpha-form of DNA are based on the pucker on the sugar ribose. As DNA doesn't have a 2'-OH, it can obtain both conformations. RNA does not have this luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus constraining the RNA to adopt the A-form. Incidentally this steric limitation is ...


9

To address your list: a high quality 3D structure: this you can easily get from PDB, using the answers to the question you linked as starting point. However, it is become increasingly clear that intrinsically unstructured proteins also play important roles in the cell, and for these you won't get a good 3D structure. known activity in vivo / known ...


8

Try to pass the matrix as a String containing 18 floats separated by commas, e.g. like cmd.set_view (''' 0.590180993, 0.670941532, 0.448923886,\ -0.507570565, 0.740831316, -0.439937204,\ -0.627747774, 0.031782545, 0.777776182,\ 0.000000000, 0.000000000, -417.497009277,\ 0.741809845, 7.078243256, 16.473480225,\ ...


7

With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).


7

I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including: Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170 Ali et al ...


6

Crystallography requires the collection of many measurements (could be a few thousand to even millions depending on the size of the molecule and complexity of the crystal (technically speaking, the size of the crystal's unit cell is a major determining factor for the size of the data set). I'm not going to assume this is a small molecule crystal like a salt ...


6

This is not my field so I'm risking a wrong/incomplete answer here, but I'd say that the critical difference is the almost complete occurrence of double-stranded DNA that precludes the formation of the tertiary structures in single-stranded RNA, rather than the 2'OH difference. In fact, and following the link you posted, the authors even comment in the ...


6

You cannot solve a structure with a single frame, even with perfect diffraction. The reason you need images over a large swath of angles is because the diffraction pattern is also in three dimensions, in the so-called "reciprocal space". At minimum, a 180° rotation of the crystal is needed to sweep the entire reciprocal space sphere with the plane of ...


6

There is indeed a repulsive force between the phosphates in the DNA backbone. (The pK of the phosphate is very low so it will be ionised at all physiologically-relevant pH.) This is why DNA behaves like a stiff rod over short distances. However cations in solution will help to shield some of this repulsion. This is why DNA melting temperature decreases as ...


6

Ventricaria ventricosa (previously called Valonia ventricosa) is not exactly a single cell. It has a coenocytic structure with multiple nuclei and chloroplasts. As Jasand Pruski correctly guessed the organism possesses a large central vacuole which is multilobular in structure (lobules radiating from a central spheroid region). The entire cell contains ...


6

Parallel DNA helix can exist and this has been observed experimentally. However these structures are stabilized by Hoogsteen type base pairing [1,2] and not the usual Watson-Crick type pairing because the parallel conformation does not allow the latter (See the figure below). This elongates the hydrogen bonds and also causes a loss of one hydrogen bond ...


5

Hi sorry i missed this one - not too hard for "biology" If you look at a protein crystal (or any crystal really) in an x-ray beam, it scatters lots of spots (diffraction reflections). If you look at a picture of crystalline diffraction, at larger angles from the center of the x-ray beam, the reflections get weaker and weaker and basically just stop, if the ...


5

You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example: . .... Because, from: http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html procedure: hilight_binding_site (imol, centre_residue_spec, hilight_colour, radius): hilight-colour is specified in degrees ...


5

ProDy works quite well, especially from within an existing Python script. The following code takes an existing PDB file, performs some selection query on it, then saves it to another file. import prody def pdbsubset(inpdb, outpdb, selection): with open(inpdb) as protf: prot = prody.parsePDBStream(protf) atoms = prot.select(selection) ...


5

Protein structures, which can be obtained from protein crystals or from concentrated solutions of pure protein via NMR, are arguably the primary source of knowledge that we have about how genes perform their function on the molecular level. I've added a link to RCSB.org above - they write up a story on an important protein structure monthly(?) - its a ...


5

I think you have misunderstood the "inside" part of the "positive-inside rule". Perhaps because "inside" is indeed an imprecise term (but now it is history and cannot be changed ;) ). In order to understand it a bit better it helps to think about the topology of the membrane. During synthesis most membrane proteins (ignoring peroxisomal and mitochondrial ...


5

This is purely coincidental. The term levo simply means the direction that the pure enantiomer of the compound rotates plane polarized light at a specific wavelength and has no direct bearing on the interactions with biological systems. A quick search of the Dictionary of Drugs database gave 6845 compounds with optical rotation >0 (dextro-compounds) and 8406 ...


4

I only know of one method, but here it is. You create a sphere the diameter of the VdW radius of water, and then 'roll' it along the surface. I know this as a Richards-Lee surface, wikipedia has another name for it. This looks complicated, but its not. you move the probe sphere along the surface of the molecule in the XY plane until it just touches ...


4

I don't know of any examples of this but I would say no doubt, that's quarternary structure. Quarternary isn't so much defined by the kind of interaction but much more the fact that it's between different polypeptides; all lower-level structures are within one polypeptide. (Wikipedia agrees.)


4

You can use "as" to switch to a particular style (http://pymolwiki.org/index.php/As ): as cartooon, 11AS and chain a You can also hide everything, to remove all representations (http://pymolwiki.org/index.php/Hide): hide every, 11AS and not (n. ca+c+n and resi 5-10) I'm a fairly expert user of PyMOL and I've never seen an API exposed which will show ...


4

In many cases they are available. One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors. If the question is 'why are they giving only the structure factors and not the ...


4

Chains are individual polypeptides that make up a multimeric protein complex. I'm curious as to how they are first found and what causes them? SDS-PAGE will resolve all the different chains (if they are different in molecular weight). Chains are products of translation (and some modifications such as clipping and/or other PTMs etc) and they assemble ...


4

DNA is not always negatively supercoiled naturally. It is important to keep in mind that different regions of topologically constrained DNA can have different supercoiling values. For example, the action of unwinding DNA for transcription or replication introduces positive supercoils ahead of the polymerase and negative supercoils behind it. Additionally, ...


4

Aligning in PyMol PDB ID 1h9t contains a structure of both a DNA and a protein. It starts as one object. Before we perform an alignment, we need to separate your DNA from the protein. Show sequence (click the S at the bottom right). Highlight all the "residues" from the chains X and Y (these chains contain each strand of your DNA) in the sequence ...


3

If I understand the question correctly, you're thinking something along the lines of modular tertiary domains, but in a quaternary sense? For a reversible interaction, heterotrimeric G proteins spring to mind. Once activated by a G protein coupled receptor (GPCR), the alpha subunit and the beta-gamma complex dissociate from the receptor and from each ...


3

I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds. Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g., jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS") Step 2: Only display the hbonds jmolScriptWait("display connected(hbond)") Step 3: Export the ...



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