4EJL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.445 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small molecule regulation of protein conformation by binding in the Flap of HIV protease.

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.

(2013) Acs Chem.Biol. 8: 1223-1231

  • DOI: 10.1021/cb300611p
  • Primary Citation of Related Structures:  

  • 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 ac ...

    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.


    Organizational Affiliation

    Deparatment of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute , 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype DMutation(s): 5 
Gene Names: gag-pol
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D)
Go to UniProtKB:  P12499
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IOP
Query on IOP

Download SDF File 
Download CCD File 
A
INDOLYLPROPIONIC ACID
C11 H11 N O2
GOLXRNDWAUTYKT-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IOPIC50: 10 nM (84) BINDINGDB
IOPKd: 7200 nM BINDINGMOAD
IOPKd: 7200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.445 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 28.815α = 90.00
b = 65.910β = 90.00
c = 92.514γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
SAINTdata reduction
MOLREPphasing
SAINTdata scaling
PROTEUM PLUSdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection