Hi~ i am a new member here... Have some questions in mind to ask, hope your can help me.... :) How 3D structure can be useful?

For 3D structural information on your protein of interest go to

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=structure

In your case, you should search form "collagen".

That will find 78 PDB protein files. You can find the ones that are of most interest to you and save them to your own computer. Then you will need an application like Deep View (freeware found at http://swissmodel.expasy.org/spdbv/text/download.htm) to view these files.

3D structures are extremely valuable, because they allow the researcher to visualize the key structural and functional regions of the molecule in a conformation that is likely to be very close to its state, or one of its states in vivo. One can see how particular residues interact with substrate in enzyme or ion binding pockets. The distances between residues that have been hypothesized to associate by disulphide bonds, H-bonds, or cation-pi interactions can also be measured and the theory proved or disproved. Some molecules can be crystalized in mutliple states, so that one can see the important molecular rearrangement when a molecule is in the active (e.g. enzyme bound, or open channel) or inactve (not bound to enzyme, closed or desensitized channel). Crystallography can also allow the visualization of some protein structure that cannot be predicted by looking at the primary amino acid sequence alone.

For books on this matter see

Practical Protein Crystallography
by Duncan E. McRee
ISBN: 0124860524


Principles of Protein X-ray Crystallography (Springer Advanced Texts in Chemistry)
by Jan Drenth
ISBN: 0387985875

Crystallization of Biological Macromolecules
by Alexander McPherson
ISBN: 0879696176

Protein Crystallography (Molecular Biology Series)
ISBN: 0121083500

Preparation and Analysis of Protein Crystals
by Alexander McPherson
ISBN: 089464355X

Protein Crystallography in Drug Discovery (Methods and Principles in Medicinal Chemistry)
by Robert E. Babine, Sherin S. Abdel-Meguid, Raimund Mannhold, Hugo Kubinyi, Gerd Folkers
ISBN: 3527306781

Introduction to Protein Structure
by Carl-Ivar Branden, John Tooze
ISBN: 0815323050

I dont work in the field, but from my original reply you wll see there are 78 crystal structures in the protein databank that are part of collagen or related to collagen. There are also many papers on the subject of colagen structure that can be found by performing a PubMed search (even a Google search!).

To get a definitive answer to your question you are going to have to do your own literature search and review to get your answer. Welcome to Research.

"Elly - Via PM" said:

Hi! I have encountered a problem on Collagen file format. What are the types of file format i can used and how are the file formats being created? Pls help me! thanks alot! :)

PDB files are text files, which can be human read, following display in any text editor or even a web-browser. They contain information about the protein, references, etc first, followed by co-ordinates which describe the 3D structure of the protein.

There are various applications - for all platforms and operating systems - which can display these co-ordinates in various ways so that you can easily interpret this data. As FraserMoss suggested - Deep View - the swissprot database viewer - [url]http://www.expasy.org/spdbv/ is a good one to start with - RasMol is even simpler.

As for where the data comes from - this is covered in the links I provided in reply to your crossposting on another forum.
http://www.scientistsolutions.com/index.php?a=topic&t=1199

See:
http://en.wikipedia.org/wiki/X-ray_crystallography

NMR is another method for obtaining structural data - and you will find NMR and X-Ray crystallography derived structures - as well as computer / human predicted structures in the PDB.