<< Chapter < Page Chapter >> Page >
This is an introduction to the Protein Data Bank (PDB) website, a depository for files containing experimentally-determined atomic coordinates of biological macromolecules, including nucleic acids, as well as proteins. It includes a tutorial in placing queries to the PDB and interpreting PDB files.

The Protein Data Bank (PDB) is a public domain repository containing experimentally determined structures of three-dimensional biological macromolecules. The majority of these structures have been determined by x-ray crystallography, but structures determined using nuclear magnetic resonance (NMR) methods are on the rise. A very few theoretical models are also included in the PDB. The PDB was originally established at Brookhaven National Laboratory (1) in October, 1971, with 7 structures. It is currently managed by Rutgers, (2) The State University of New Jersey, the San Diego Supercomputer Center at the University of California, San Diego, andthe Center for Advanced Research in Biotechnology/UMBI/NIST, and it stores over 29,000 structures. The European Bioinformatics Institute Macromolecular Structure Database group (UK) and the Protein Research Institute at Osaka University, Japan are international contributors to the contents of the PDB.

The name Protein Data Bank is historical in origin, because the present-day PDB includes many DNA and RNA structures as well. The most important information contained in any given PDB file is a set of 3-dimensional vectors representing the atomic coordinates for each of the individual atoms that comprise the biological molecule(s) included in the structure. These coordinates can be fed into various graphics programs that allow the scientist to view the a 3-dimensional model of molecule. An example of one of these models is the molecule of the month that can be viewed by clicking on the link in the left-hand blue border of the PDB home page .

What is the featured molecule of the month today?

Got questions? Get instant answers now!

The PDB search engine asks the user to "Enter a PDB ID or keyword". The PDB ID, which is also referred to in journal articles as the PDB accession code, is a 4 character alphanumberic ID code assigned to the structure coordinate file when it is deposited into the PDB by the experimentalist who solved the structure. For instance, the PDB ID for a 2.2 angstrom crystal structure of the protein calmodulin is 3CLN. Perform a search using 3CLN as the query. The result is a summary page that lists the method of structure determination, as well as the authors of the structure. It is not uncommon for the authors of the primary citation to differ somewhat from the authors of the structure, as the first refers to the writer(s) of the article where the new structure first appeared and the second refers to the experimentalist(s) who determined the structure of the deposited molecule(s). The compound field identifies the common name of the protein or nucleic acid molecule in the structure, and the source identifies the genus and species of the organism from which this molecule is derived, which in this case is a rat. At the bottom of the summary, is a table entitled HET groups. HET (heteroatom) refers to any atom that is not part of the biological molecule(s) in the structure.These are often ligands, which are molecules that commonly bind the particular protein or nucleic acid in the structure. In this case, there is calcium in the structure, which may not be surprising, given that the classification listed for this protein in the summary is "Calcium Binding Protein". The formula column of this table gives the chemical formula of the ligand.

Questions & Answers

A golfer on a fairway is 70 m away from the green, which sits below the level of the fairway by 20 m. If the golfer hits the ball at an angle of 40° with an initial speed of 20 m/s, how close to the green does she come?
Aislinn Reply
cm
tijani
what is titration
John Reply
what is physics
Siyaka Reply
A mouse of mass 200 g falls 100 m down a vertical mine shaft and lands at the bottom with a speed of 8.0 m/s. During its fall, how much work is done on the mouse by air resistance
Jude Reply
Can you compute that for me. Ty
Jude
what is the dimension formula of energy?
David Reply
what is viscosity?
David
what is inorganic
emma Reply
what is chemistry
Youesf Reply
what is inorganic
emma
Chemistry is a branch of science that deals with the study of matter,it composition,it structure and the changes it undergoes
Adjei
please, I'm a physics student and I need help in physics
Adjanou
chemistry could also be understood like the sexual attraction/repulsion of the male and female elements. the reaction varies depending on the energy differences of each given gender. + masculine -female.
Pedro
A ball is thrown straight up.it passes a 2.0m high window 7.50 m off the ground on it path up and takes 1.30 s to go past the window.what was the ball initial velocity
Krampah Reply
2. A sled plus passenger with total mass 50 kg is pulled 20 m across the snow (0.20) at constant velocity by a force directed 25° above the horizontal. Calculate (a) the work of the applied force, (b) the work of friction, and (c) the total work.
Sahid Reply
you have been hired as an espert witness in a court case involving an automobile accident. the accident involved car A of mass 1500kg which crashed into stationary car B of mass 1100kg. the driver of car A applied his brakes 15 m before he skidded and crashed into car B. after the collision, car A s
Samuel Reply
can someone explain to me, an ignorant high school student, why the trend of the graph doesn't follow the fact that the higher frequency a sound wave is, the more power it is, hence, making me think the phons output would follow this general trend?
Joseph Reply
Nevermind i just realied that the graph is the phons output for a person with normal hearing and not just the phons output of the sound waves power, I should read the entire thing next time
Joseph
Follow up question, does anyone know where I can find a graph that accuretly depicts the actual relative "power" output of sound over its frequency instead of just humans hearing
Joseph
"Generation of electrical energy from sound energy | IEEE Conference Publication | IEEE Xplore" ***ieeexplore.ieee.org/document/7150687?reload=true
Ryan
what's motion
Maurice Reply
what are the types of wave
Maurice
answer
Magreth
progressive wave
Magreth
hello friend how are you
Muhammad Reply
fine, how about you?
Mohammed
hi
Mujahid
A string is 3.00 m long with a mass of 5.00 g. The string is held taut with a tension of 500.00 N applied to the string. A pulse is sent down the string. How long does it take the pulse to travel the 3.00 m of the string?
yasuo Reply
Who can show me the full solution in this problem?
Reofrir Reply
Got questions? Join the online conversation and get instant answers!
Jobilize.com Reply

Get Jobilize Job Search Mobile App in your pocket Now!

Get it on Google Play Download on the App Store Now




Source:  OpenStax, Bios 533 bioinformatics. OpenStax CNX. Sep 24, 2008 Download for free at http://cnx.org/content/col10152/1.16
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'Bios 533 bioinformatics' conversation and receive update notifications?

Ask