ACT Protein Data Bank Discussion Questions

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Description

Open up the Protein Data Bank (PDB) website, https://www.rcsb.org/ and search code 3DZY which is the structure for Intact PPAR gamma

1. Does this protein complex have beta-sheets?

2. What residues on RXRalpha are involved in contacting Thr 440 on the PPARgamma protein? What kind of an interaction is it?

biochem_pdb.pdf

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Explanation & Answer

View attached explanation and answer. Let me know if you have any questions.

Receptor Complex on DNA bound with Rosiglitazone, 9-cis Retinoic Acid and NCOA2
Peptide. You can use the builtin molecular viewer or you can use your favorite molecular
viewer such as Chimera, Pymol or VMD. Do your best to answer the following questions
about the structure.
1. Does this protein complex have beta-sheets?
This protein doesn’t have beta-sheets protein complex. However, the PPAR-gamma and RXRalpha largely combines in a non-symmetric complex. This is important and critical to help and
allow PPAR-gamma ligand-binding domain or LBD to have a contact multiple in the overall
protein domains.
2. What residues on RXRalpha are involved in contacting Thr 440 on the
PPARgamma protein? What kind of an interaction is it?
Preferably, the residues involved in this contact include Asn 160 from PPAR-γ, Gln 206 and Arg
209 of RXR-α. Notably, the interaction happens between the RXR-α and PPAR-γ DBDs via the
minor spacer groove. Importantly, the DBD-DBD DNA dependence contacts is described and
defined to be as clear as the overall two proteins often buried in a modest 30 A surface area
existing between the two norms. The arrangement interpretation largely conforms that PPRE
DNA has the capability to allosterically adds its own binding in this process. In this case, the
norm allows it to directly bridge the gap that exists between the two overall receptor DBDs. Thus,
the existing interaction in this process is DBD-DBD DNA dependence contacts.

Please view explanation and answer below.

Directions: Open up the Protein Data Bank (PDB) website, https://www.rcsb.org/ and
search code 3DZY which is the structu...

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