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Questions tagged [structural-biology]

For questions related to the molecular structure of biological macromolecules (especially proteins and nucleic acids), how they acquire the structures they have, and how alterations in their structures affect their function.

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28 votes
2 answers
14k views

Confusion about direction of dipole arrow in alpha-helices and other molecules

I understand that molecular dipoles are electric dipoles. And electric dipole moment vectors point from the negative to the positive charge. In class we learned to draw these special molecular dipole ...
Reto Höhener's user avatar
2 votes
2 answers
138 views

How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
Gunther Schadow's user avatar
0 votes
1 answer
75 views

Modelling planar molecules and their evolutions

I am trying to simulate a chain of molecules which are planar. Can anyone please give me an example of the molecular chain which can stay as planar with it's minimum energy state is planar. A ...
Omar Shehab's user avatar
19 votes
2 answers
2k views

How large is the energy difference between keto- and enol-form of guanine and uracil?

The nucleobases in DNA and RNA are generally present in the keto-form, and not in the enol-form. As an interesting historical note, James Watson and Francis Crick did initially believe them to adopt ...
Mad Scientist's user avatar
16 votes
1 answer
3k views

What is Cβ (C-beta) deviation?

Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some ...
Nick T's user avatar
  • 2,563
15 votes
1 answer
14k views

Why/how is blood red? (colours of hemoglobin)

Oxyhaemoglobin is red, deoxyhaemoglobin is bluish-purple, and carboxyhaemoglobin is a cherry red colour. Evidently in the porphyrin around the iron molecule in heme there is a conjugated $\pi$-system ...
James Harrison's user avatar
5 votes
1 answer
411 views

Is the structure of a crystalized protein the native one?

When one finds the 3D structure of a protein by crystalizing it and then making a X-ray experiment, how does one know that the geometrical configuration of the crystal is the same (or even close) to ...
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