4EJK

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1-N in the outside/top of flap

Summary for 4EJK

• Entry DOI: 10.2210/pdb4ejk/pdb
• Related: 4EJ8 4EJD 4EJL
• Related PRD ID: PRD_000557
• Descriptor: Protease, pepstatin, INDOLYLPROPIONIC ACID, ... (4 entities in total)
• Functional Keywords: apo protease, allostery, fragment binding, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Human immunodeficiency virus 1
• Cellular location: Gag-Pol polyprotein: Host cell membrane; Lipid-anchor. Matrix protein p17: Virion membrane; Lipid- anchor . Capsid protein p24: Virion . Nucleocapsid protein p7: Virion . Reverse transcriptase/ribonuclease H: Virion . Integrase: Virion : P12499
• Total number of polymer chains: 3
• Total formula weight: 22538.77

Authors

Tiefenbrunn, T.,Stout, C.D. (deposition date: 2012-04-06, release date: 2013-05-01, Last modification date: 2018-03-07)

Primary citation

Tiefenbrunn, T.,Forli, S.,Baksh, M.M.,Chang, M.W.,Happer, M.,Lin, Y.C.,Perryman, A.L.,Rhee, J.K.,Torbett, B.E.,Olson, A.J.,Elder, J.H.,Finn, M.G.,Stout, C.D.
Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
Acs Chem.Biol., 8:1223-1231, 2013

PubMed Abstract: The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the Tm of apo-PR by 3.5-5 °C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR.

PubMed: 23540839
DOI: 10.1021/cb300611p

Experimental method

X-RAY DIFFRACTION (1.794 Å)