1FAV

THE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR IN COMPLEX WITH THE HIV-1 GP41 TRIMERIC CORE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core.

Zhou, G.Ferrer, M.Chopra, R.Kapoor, T.M.Strassmaier, T.Weissenhorn, W.Skehel, J.J.Oprian, D.Schreiber, S.L.Harrison, S.C.Wiley, D.C.

(2000) Bioorg.Med.Chem. 8: 2219-2227


  • PubMed Abstract: 
  • The three-dimensional structure of the complex between an HIV-1 cell-entry inhibitor selected from screening a combinatorial library of non-natural building blocks and the central, trimeric, coiled-coil core of HIV-1 gp41 has been determined by X-ray ...

    The three-dimensional structure of the complex between an HIV-1 cell-entry inhibitor selected from screening a combinatorial library of non-natural building blocks and the central, trimeric, coiled-coil core of HIV-1 gp41 has been determined by X-ray crystallography. The biased combinatorial library was designed to identify ligands binding in nonpolar pockets on the surface of the coiled-coil core of gp41. The crystal structure shows that the non-peptide moiety of the inhibitor binds to the targeted cavity in two different binding modes. This result suggests a strategy for increasing inhibitor potency by use of a second-generation combinatorial library designed to give simultaneous occupancy of both binding sites.


    Organizational Affiliation

    Laboratory of Molecular Medicine, The Children's Hospital, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 ENVELOPE PROTEIN CHIMERA
A
79Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Human immunodeficiency virus type 1 group M subtype B
This entity is chimeric
Mutation(s): 8 
Gene Names: GCN4 (AAS3, ARG9), env
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P03069
Find proteins for P03377 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03377
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)
C
33Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
GGL
Query on GGL
C
L-gamma-peptide, C-delta linkingC5 H9 N O4

--

4BA
Query on 4BA
C
NON-POLYMERC11 H13 N O4

--

3PA
Query on 3PA
C
NON-POLYMERC8 H14 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.240 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 35.819α = 90.00
b = 35.819β = 90.00
c = 164.691γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-09
    Type: Advisory, Refinement description, Source and taxonomy