2J9J

Atomic-resolution Crystal Structure of Chemically-Synthesized HIV-1 Protease Complexed with Inhibitor JG-365


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.191 
  • R-Value Observed: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Insights from Atomic-Resolution X-Ray Structures of Chemically Synthesized HIV-1 Protease in Complex with Inhibitors.

Johnson, E.C.B.Malito, E.Shen, Y.Pentelute, B.Rich, D.Florian, J.Tang, W.J.Kent, S.B.H.

(2007) J Mol Biol 373: 573

  • DOI: 10.1016/j.jmb.2007.07.054
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The human immunodeficiency virus 1 (HIV-1) protease (PR) is an aspartyl protease essential for HIV-1 viral infectivity. HIV-1 PR has one catalytic site formed by the homodimeric enzyme. We chemically synthesized fully active HIV-1 PR using modern lig ...

    The human immunodeficiency virus 1 (HIV-1) protease (PR) is an aspartyl protease essential for HIV-1 viral infectivity. HIV-1 PR has one catalytic site formed by the homodimeric enzyme. We chemically synthesized fully active HIV-1 PR using modern ligation methods. When complexed with the classic substrate-derived inhibitors JG-365 and MVT-101, the synthetic HIV-1 PR formed crystals that diffracted to 1.04- and 1.2-A resolution, respectively. These atomic-resolution structures revealed additional structural details of the HIV-1 PR's interactions with its active site ligands. Heptapeptide inhibitor JG-365, which has a hydroxyethylamine moiety in place of the scissile bond, binds in two equivalent antiparallel orientations within the catalytic groove, whereas the reduced isostere hexapeptide MVT-101 binds in a single orientation. When JG-365 was converted into the natural peptide substrate for molecular dynamic simulations, we found putative catalytically competent reactant states for both lytic water and direct nucleophilic attack mechanisms. Moreover, free energy perturbation calculations indicated that the insertion of catalytic water into the catalytic site is an energetically favorable process.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, IL 60637, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE
A
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for O38907 (Human immunodeficiency virus 1)
Go to UniProtKB:  O38907

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEASE
B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for O38907 (Human immunodeficiency virus 1)
Go to UniProtKB:  O38907
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
INHIBITOR MOLECULE JG365
C
7synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000228 (01D)
Query on PRD_000228
CJG-365Peptide-like /  Inhibitor

--

Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
NLE
Query on NLE
A, B
L-PEPTIDE LINKINGC6 H13 N O2LEU
SLZ
Query on SLZ
A, B
L-PEPTIDE LINKINGC5 H12 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.191 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.548α = 90
b = 58.814β = 90
c = 60.889γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Other, Source and taxonomy, Structure summary
  • Version 1.3: 2013-03-06
    Changes: Other
  • Version 1.4: 2017-02-15
    Changes: Source and taxonomy
  • Version 1.5: 2017-10-18
    Changes: Advisory, Data collection
  • Version 1.6: 2019-05-22
    Changes: Data collection, Derived calculations, Refinement description