6 votes
Accepted

Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

As far as I am aware, there is no known requirement for Cd in mammalian systems, but it is extremely toxic (Waalkes & Goering). It would seem that cadmium is required to get crystals of RBP, and ...
user338907's user avatar
  • 4,723
5 votes

Why are there so few full-length antibody structures?

There IS a problem! In a previous version of this answer I focussed on various historical, technical, goal-related and commercial reasons for the predominance of structures of antibody fragments (Fab ...
David's user avatar
  • 25.7k
5 votes
Accepted

Protein crystal X-ray diffraction at room temperature?

While protein diffraction data is nowadays most often collected in cryogenic temperatures, the room temperature crystallography also exists and you can find thousands of datasets in the PDB that were ...
marcin's user avatar
  • 449
5 votes
Accepted

Proteins in water vs proteins in crystal

Protein crystals are not like crystals of more commonly found substances like salt [NaCl] or diamond [carbon only.] These materials do not include other atoms in their crystal structures. For ...
Edward Kowal's user avatar
4 votes
Accepted

NAG, FUC molecules in PDB files

The insulin receptor is a glycoprotein. This is discussed, albeit briefly, in both papers for the structures you mentioned and the glycosylation is visible in the structures themselves. You can get ...
canadianer's user avatar
  • 17.7k
3 votes

Can protein structure be determined by X-Ray Diffraction in a single image?

Can protein structure be determined by X-Ray Diffraction in a single image? Yes. Using a technique called Laue diffraction, it is possible to obtain sufficient data from a single image to solve a ...
Karsten Theis's user avatar
3 votes
Accepted

Why are there so few full-length antibody structures?

The more flexible a molecule, the more difficult it is to get a crystallization that actually tells you something about the molecule's free-phase arrangement/behavior. Basically (the best) ...
the gods from engineering's user avatar
3 votes

What are the benefits of elucidating the three-dimensional structure of a protein?

Why study protein structure? “What is the secret of life?’ I asked. ‘I forget,’ said Sandra. ‘Protein,’ the bartender declared. ‘They found something out about protein.‘ ‘Yeah,’ said Sandra, ‘that’s ...
David's user avatar
  • 25.7k
3 votes
Accepted

Subset of Protein Crystal Structures (from PDB)

Richardsons' Lab has a top8000 list. See their paper from 2016. They also have top500 list, but it hasn't been updated for many years.
marcin's user avatar
  • 449
2 votes

NAG, FUC molecules in PDB files

Apologia This addresses the general case, rather than the particular case of the insulin receptor, which is answered by @canadianer. The General Problem of unexpected ligands in PDB structures In ...
David's user avatar
  • 25.7k
2 votes
Accepted

Generate mesh surface from protein structure

PyMOL and Chimera can do that, and both can be script-driven. The PyMOL wiki is full of examples, and probably already has some how-to that would get you started. Chimera also has a complete ...
Guillaume's user avatar
  • 715
2 votes

Techniques for detecting phosphorylation sites in proteins?

X-ray crystallography has been used to detect phosphorylated sites. The RCSB protein database currently contains 856 structures that have both a resolution below 3 angstroms and the keyword "...
Michael_A's user avatar
  • 1,305
2 votes
Accepted

Techniques for detecting phosphorylation sites in proteins?

In principle X-ray crystallography or NMR could detect phosphorylation sites but they are much more complex and expensive techniques than mass spec. So for simply figuring out phosphorylation patterns ...
Thawn's user avatar
  • 1,239
1 vote

Why are there so few full-length antibody structures?

There are thousands of structures in the PDB of neutralizing antibodies against all sorts of viruses using all sorts of methods (NMR,x-ray,electron microscopy) as complex or stand alone. I guess your ...
KaPy3141's user avatar
  • 1,597
1 vote

Using BLAST for molecular replacement in structural biology

Identity, Similarity, E-value are the key numbers, for the prediction of the 3D structure of proteins. The Length of the query and selected results should also be close to each other. E-value: The ...
Amirreza Mousavi's user avatar

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