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Learning to navigate the RCSB PDB website
Searching from the top-bar
1. Open the RCSB PDB website (www.pdb.org). Type “4hhb” next to the box PDB ID or
Text in the top search bar and click on the Search button. You should be directed to the
structure summary page for the PDB entry 4HHB.
a. What is the molecule in this PDB entry?
The crystal structure of human deoxyhaemoglobin.
b. What year was this PDB entry released?
1984
c. What experimental method was used to solve the structure in this entry?
X-ray diffraction
d. How many polymeric chains are present in this entry?
4 but only 2 are sequence unique
e. Name 2 ligands that are present in this entry.
1. Protoporphyrin IX containing Fe (HEM)
2. Phosphate ion (PO4)
f. What is the most common secondary structural element seen in the polymers of
this entry. (Hint: see the sequence tab or visualize the structure in Jmol)
Alpha helices
2. Go back to the top search bar. Type “Hemoglobin” next to the box PDB ID or Text and
click on the Search button. You should see a query results browser page.
a. How many structures match this query?
532
b. What is the most common source organism? (Hint: Click on the Organism box in
the Query Refinements section on the top of the Query Results Browser page)
Human at 39.4%
c. Sort the results by “Release date” using the Sort by pull down menu. What is the
PDB ID of the earliest released hemoglobin structure? When was it released?
1FDH; 1976
d. Create an Image Collage using the Generate Reports pull-down menu (under
Custom Reports). Can you identify any 1 structure that has beta sheet structure?
What is this structure (include the PDB ID)?
1B2V Heme binding protein A
e. Did you expect to see this structure when you searched for “Hemoglobin”?
Explain.
Yes. If one does not narrow his/her search, the results will include all structures
related to hemoglobin (like this transport protein, for example).
3. Hemoglobin molecules have Heme groups bound to the protein. In the top search bar,
select Chemical Name from the pull-down menu. Type “Heme” and click on the Search
button.
a. How many ligands match this query? Give 2 examples and include the 3 letter
codes.
Shuchi
8 ligands; e.g. 2-Phenylheme (2FH) and CIS-Heme D Hydroxychlorin Gamma
Spirolactone (HDD)
b. What is the 3 letter code of the most popular Heme in the PDB? (Hint: Look for
the ligand with the maximum number of structures associated with it). How many
entries are associated with this ligand?
HEM 2564 associated structures
c. Click on the list of structures with the most popular Heme ligand. Name any 2
proteins (other than Hemoglobin) that have this ligand bound to it.
Human Type B Cytochrome b5 (3NER) and Staphylococcus aurius heme-bound
IsdB-N2 (3RTL)
Advanced Search:
4. Click on the Advanced Search button in the top search bar. A new page will open up with
options to run customized queries.
a. Choose a Query Type > Macromolecule Name (under Structure Annotation).
Type “Hemoglobin” in the box that opens up for the macromolecule name. Click
on the Result Count box. How many structures match this part of the query?
490
b. How does this number compare to the number of “hemoglobin” structures
returned from the top search bar text-search with “Hemoglobin” (question 2a)?
The above number is fewer (467 vs 504). This difference is due to the fact that the
full text search includes files where “Hemoglobin” appears anywhere in the header
section of the PDB file.
532 vs 490
c. Click on the + sign in the Add Search Criteria bar. This should open a box to
include additional query criteria. Find the first hemoglobin structure deposited by
Max Perutz. (Hint: Add Search Critera > Author Name > “Perutz” > Submit
Query)
1FDH 1976
d. From the left hand menu, look under Results > Query History. Select the query
results for “Molecule Name Search : Molecule Name=hemoglobin”. Are there
any structures in the result list that are not true hemoglobins? Give 2 examples.
(Hint: Check out the Enzyme Classification Query Refinement options).
Crystal strucure of Plasmepsin I (3QRV) and Integral membrane domain of
autotransporter Hbp (3AEH)
Sequence Search:
5. Type “1ZAA” in the top search box to open the structure summary page.
a. Describe the contents of this entry in words.
The entry contains a structure which consists of 3 chains: 2 DNA strands bound by a
ZIF268 protein (zinc finger). The ligand of the structure is the zinc ion which forms a
coordination complex with the atoms to which it is attached. This structure is used in
DNA transcription and was found in the common house mouse. It was discovered and
realeased by Pavletich and Pabo in 1993 using a resolution of 2.10 angstroms.
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b. From the Advanced Search Interface select Sequence Features > Sequence search
(BLAST or FASTA). Type “1ZAA” in the Structure ID box. Select chain ID “C”
and click on Result Count. How many structures match this query?
189
c. Before clicking on the Submit Query button check on the Remove Similar
Sequences box at 30% Identity. How many structures match this query? Explain
the difference in number reported in answers 5b and 5c
55 results. Structures that are at least 30% similar will be represented by one
structure, decreasing the number of resulting entries.
d. Can you quickly figure out what most of these proteins do? (Hint: check the GO
Hits tab)
DNA transcription or DNA binding
Other Search Options:
6. Most structures in the PDB are described in a journal article, called the primary citation.
The PDB entry may also be referred in other publication. Which journal is the maximum
number of primary citations published in? (Hint: try using the Search > Histograms
options from the left hand menu.)
The Journal of Molecular Biology with 9022 items
7. Based on SCOP and CATH classification (hint: use the Browse Database option in the
left hand menu),
a. Does the PDB presently have more structures that are mostly/all alpha or
mostly/all beta?
Mostly beta
b. How do the number of all/mainly alpha, all/mainly beta structures compare with
the alpha beta structures? Give approximate proportions.
The CATH mainly alpha and mainly beta structures each have structure numbers
equal to approximately half that of alpha beta structures.
The SCOP all alpha compared to alpha beta strucutes proportion is approximately
2/3. The beta compared to alpha beta structures proportion is about 5/6.