<< 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

how do they get the third part x = (32)5/4
kinnecy Reply
can someone help me with some logarithmic and exponential equations.
Jeffrey Reply
sure. what is your question?
okay, so you have 6 raised to the power of 2. what is that part of your answer
I don't understand what the A with approx sign and the boxed x mean
it think it's written 20/(X-6)^2 so it's 20 divided by X-6 squared
I'm not sure why it wrote it the other way
I got X =-6
ok. so take the square root of both sides, now you have plus or minus the square root of 20= x-6
oops. ignore that.
so you not have an equal sign anywhere in the original equation?
Commplementary angles
Idrissa Reply
im all ears I need to learn
right! what he said ⤴⤴⤴
what is a good calculator for all algebra; would a Casio fx 260 work with all algebra equations? please name the cheapest, thanks.
Kevin Reply
a perfect square v²+2v+_
Dearan Reply
kkk nice
Abdirahman Reply
algebra 2 Inequalities:If equation 2 = 0 it is an open set?
Kim Reply
or infinite solutions?
The answer is neither. The function, 2 = 0 cannot exist. Hence, the function is undefined.
Embra Reply
if |A| not equal to 0 and order of A is n prove that adj (adj A = |A|
Nancy Reply
rolling four fair dice and getting an even number an all four dice
ramon Reply
Kristine 2*2*2=8
Bridget Reply
Differences Between Laspeyres and Paasche Indices
Emedobi Reply
No. 7x -4y is simplified from 4x + (3y + 3x) -7y
Mary Reply
is it 3×y ?
Joan Reply
J, combine like terms 7x-4y
Bridget Reply
how do you translate this in Algebraic Expressions
linda Reply
Need to simplify the expresin. 3/7 (x+y)-1/7 (x-1)=
Crystal Reply
. After 3 months on a diet, Lisa had lost 12% of her original weight. She lost 21 pounds. What was Lisa's original weight?
Chris Reply
what's the easiest and fastest way to the synthesize AgNP?
Damian Reply
types of nano material
abeetha Reply
I start with an easy one. carbon nanotubes woven into a long filament like a string
many many of nanotubes
what is the k.e before it land
what is the function of carbon nanotubes?
I'm interested in nanotube
what is nanomaterials​ and their applications of sensors.
Ramkumar Reply
what is nano technology
Sravani Reply
what is system testing?
preparation of nanomaterial
Victor Reply
Yes, Nanotechnology has a very fast field of applications and their is always something new to do with it...
Himanshu Reply
good afternoon madam
what is system testing
what is the application of nanotechnology?
In this morden time nanotechnology used in many field . 1-Electronics-manufacturad IC ,RAM,MRAM,solar panel etc 2-Helth and Medical-Nanomedicine,Drug Dilivery for cancer treatment etc 3- Atomobile -MEMS, Coating on car etc. and may other field for details you can check at Google
anybody can imagine what will be happen after 100 years from now in nano tech world
after 100 year this will be not nanotechnology maybe this technology name will be change . maybe aftet 100 year . we work on electron lable practically about its properties and behaviour by the different instruments
name doesn't matter , whatever it will be change... I'm taking about effect on circumstances of the microscopic world
how hard could it be to apply nanotechnology against viral infections such HIV or Ebola?
silver nanoparticles could handle the job?
not now but maybe in future only AgNP maybe any other nanomaterials
I'm interested in Nanotube
this technology will not going on for the long time , so I'm thinking about femtotechnology 10^-15
can nanotechnology change the direction of the face of the world
Prasenjit Reply
At high concentrations (>0.01 M), the relation between absorptivity coefficient and absorbance is no longer linear. This is due to the electrostatic interactions between the quantum dots in close proximity. If the concentration of the solution is high, another effect that is seen is the scattering of light from the large number of quantum dots. This assumption only works at low concentrations of the analyte. Presence of stray light.
Ali Reply
the Beer law works very well for dilute solutions but fails for very high concentrations. why?
bamidele Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
Privacy Information Security Software Version 1.1a
Got questions? Join the online conversation and get instant answers!
QuizOver.com Reply

Get the best Algebra and trigonometry course in your pocket!

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?