wwpdb.org - Worldwide PDB (Protein Data Bank)

Molecule Tutorials - Herong's Tutorial Examples

∟wwpdb.org - Worldwide PDB (Protein Data Bank)

This section provides a quick introduction of the SDF (Structure Data File) format. An example of SDF file is also provided.

What Is wwpdb.org? - wwpdb.org is the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. wwpdb.org was initially established in 1971 as the Protein Data Bank (PDB) at Brookhaven National Laboratory (BNL), US. Now it has more than 176,000 proteins in the archive, and maintained by the Worldwide PDB (wwPDB) foundation.

If you want to search for protein in wwpdb.org, you can use the web portal at rcsb.org.

1. Go to wwpdb.org. Click "Advanced Search" under the search box near the top of the page. The see the Advanced Search Query Builder page.

2. Open the Sequence criteria field. And enter "NLYIQWLKDGGPSSGRPPPS".

3. Select "Polymer Entities" as the "Display Results as" format. And click "search" icon. You see matched protein entries displayed in the results area.

4. Look at the first protein entry. You see the following information. Notice that this entry has PDB ID of "1L2Y". And the query sequence matches the chain A of entity 1 of this entry 100%.

1L2Y: Entity 1: Chain A
NMR Structure of Trp-Cage Miniprotein Construct TC5b
Neidigh, J.W., Fesinmeyer, R.M., Andersen, N.H.
(2002) Nat Struct Biol 9: 425-430

Released  2002-05-29
Method  SOLUTION NMR
Organism
Macromolecule  TC5b
Sequence Match  Sequence Identity: 100%, E-Value: 1.111e-8, Region: 1-20

QUERY:  NLYIQWLKDGGPSSGRPPPS
1L2Y_1: NLYIQWLKDGGPSSGRPPPS

5. Click "3D View" on the left. You can zoom in and rotate the 3D ribbon diagram of this protein structure.

6. Look at the next entry. Its PDB ID is 2LDJ, which protein sequence matches 95% of the search sequence with one amino acid residues difference at position 10.