Introduction to MMDB and PDB 

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TUTORIAL (15-30 minutes)
 

The RCSB Protein structure Data Bank (PDB).
 
Note that the RCSB Protein Data Bank is not to be confused with the NCBI Protein Data Base! The Research Collaboratory for Structural Bioinformatics is a non-profit consortium of Rutgers University, The San Diego Supercomputer Center and the University of Wisconsin.

The Protein Data Bank (PDB) is a database of three dimensional biomolecular structures derived from X-ray crystallography and NMR-spectroscopy. Understanding the 3-dimensional shape of any molecule is essential to understanding its function. The "PDB data files"  provide the exact location of every atom in a molecule in all three dimensions (X, Y, Z). The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids.  It was established at Brookhaven National Laboratory in 1971, and originally contained only 7 structures! The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. The RCSB is a member of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniform data. Details about the history, function, progress, and future goals of the PDB can be found in About the PDB as well as in the PDB Annual Reports and PDB Newsletters.
 
 

The Molecular Modeling Database (MMDB) is a database of three dimensional biomolecular structures derived from X-ray crystallography and NMR-spectroscopy. MMDB is a subset of three dimensional structures obtained from the Brookhaven Protein DataBank (PDB), excluding theoretical models. MMDB reorganizes and validates PDB information in a way that enables cross-referencing between the chemistry and the three dimensional structure of macromolecules. Its data specification includes a description of a biopolymer's spatial structure, a description of how it is organized chemically, and a set of pointers linking the two. By integrating chemical, sequence, and structure information, MMDB is designed to serve as a resource for structure-based homology modeling and protein structure prediction. MMDB records are stored in ASN.1 format and can be displayed with the Cn3D, Rasmol, or Kinemage viewers. In addition, similar structures within the database have been identified using VAST, and new structures can be compared against the database using VAST search.


 
 		 As demonstrated earlier in these tutorials, the "Entrez Gene" data base at NCBI contains a great deal of information on DNA, transcript and protein sequence as well as conserved domains. It also contains links useful in mining data about the 3D structure and function of the gene product.

Do a search (protein) for human beta globin

Click on the image to see full-size!		 The screen with links to records for the human beta globin protein.

Click on the link for the RefSeq record (NP_000509).

Click on the image to see full-size!		 The RefSeq record has a link to structures related to human beta globin. Click on Links on the right hand side of the yellow bar and select Related Structures from the drop down menu.

Click on the image to see full-size!		 The "Related Structures" page, as shown in the thumbnail to the left, lists all the related structures, with associated information:

(From the List pull down menu select Medium redundancy)

  • A link to the structure record in the NCBI Molecular Modeling Data Base (MMDB).
  • Rollover information on the link. In the case illustrated, 2DN2 is a file which contains the structure of human beta globin at a resolution of 1.25 A0.
      • Question: What is the definition of an Angstrom? How many A0 are in a mm?
  • The red line is a graphic illustration of the structural similarity to the query protein sequence.
  • E-value (Expect value) is the number of matches that could be expected by chance in the search of the data set. The smaller the E-value, the lower the probability of a hit simply by chance.
  • A pull-down menu allows several options to limit the list.


 

Click on the image to see full-size!		 Unfortunately the MMDB link for  2DN2 does not work.(However, this may work for your protein of interest!) And this will bring you to the MMDB page where you will see a link to PDB.

The MMDB contains much of the same information as the PDB and contains a link for PDB (see thumb nail).

Click on the image to see full-size!		 You can access RCSB(PDB) directly at

http://www.rcsb.org/pdb/home/home.do 

Type 2DN2 in the search bar.

The Protein Data Bank (PDB) records also display with a number of tabs. For introductory purposes the two most relevant are:

  • Biology and Chemistry
  • Sequence Details
Underneath the graphic, there are a number of "Display Options". These are links to various viewers which can display PDB data files as an interactive graphic (the tutorial which follows will introduce WebMol).

 		 The "Biology and Chemistry Report" tab opens a screen with information about the chemical structure and biological function of the beta globin chain.

As shown in the graphic to the left, there are also links to "Entrez Gene". Finally, the cytogenetic locus (11p15.5), is provided.
 
 Click on the "Sequence Details" tab this opens a screen showing that the beta globin chain folds into a series of helices and turns. As shown in the graphic to the left, this is depicted with these secondary structures mapped onto the primary structure (amino acid sequence).

 

Click on the image to see full-size!		 Underneath the graphic, there are a number of "Display Options". These are links to various viewers which can display PDB data files as an interactive graphic (the tutorial which follows will introduce WebMol).


 
The sidebar menu offers access to additional information which is best illustrated with another structure file from PDB. 

Go back to the RCSB (PDB) home page and Enter "1HT0" into the search box, and click on the "Search" button.

  At the top of the record click on the [M] next to Learn more. This will bring you to a page with an overview of the protein and its function.

In the blue sidebar, click on the "Display Molecule" toggle. The menu which opens is shown in the thumbnail to the left. It has links to some of the viewers displayed under the graphic, but also to others such as "RasMol" and the "Swiss-PDB" viewer. Click on some of the various displays to what they look like.

 
 
 In the blue sidebar, click on the "External Links" toggle shown in the thumbnail to the left. 

A new page will open with a list of links. Scroll down the page and click on the link to "PDBSum" (near the bottom of the page).
 

Click on the image to see full-size!		 The link goes to the "Top Page" of the EBI PDBSum website. This page provides information:
  • the secondary, tertiary and quaternary structure of the protein from several aspects,
  • descriptive and taxonomic information
  • PDB files of similar structures
  • biochemistry and substrates
Click on the Protein tab at the top which brings you to the "Protein Page" of the EBI PDBSum website provides information on primary and secondary structure and the location of important functional sites. As seen on the left panel, this page has two views:  1.) "Wiring Diagram" (red circle in the thumbnail to the left);  2.) "Residue Conservation".

Click on the image to see full-size!		 Click on "Wiring Diagram".  this shows that the Chain B contains two domains, as shown in the thumbnail to the left:
  • Domain 1  (alpha-beta complex) is depicted in red. The N-terminal part of domain 1 extends from residues 1-178. The C-terminal portion of domain 1 extends from residues 318-374.
    • The 3 catalytic residues in the active site (S48, H51, L57) are shown within small red boxes.
    • Residues which interact with, and bind, the ligand are indicated with small red squares.
    • Residues which interact with, and bind, the Zinc cofactor are indicated with small blue squares.
  • Domain 2  (alpha-beta 3-layer sandwich) is depicted in blue. It extends from residues 179-317.
    • Residues which interact with, and bind, the ligand are shown.

     

Click on the image to see full-size!		 Click on "Residue Conservation". In this diagram each amino acid in Chain B is colored to indicate the degree to which it is similar to its' counterpart in similar proteins. These data are important in Comparative Genomics, because residues which are highly conserved (always the same), are very likely to participate in  the biological function of the protein. For example:
  • The 3 catalytic residues in the active site (S48, H51, L57) are highly conserved.
  • Other residues which interact with the ligand, such as 199-203, are more variable, but still more highly conserved than most.
  • Residues which interact with the Zinc, such as 97, 100 and 103, are highly conserved.
NOTE:  Be aware that such data must be considered critically ...... what are the exceptions?

 
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