2Q3I | pdb_00002q3i

Crystal structure of the D10-P3/IQN17 complex: a D-peptide inhibitor of HIV-1 entry bound to the GP41 coiled-coil pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.258 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Inhibiting HIV Entry: Discovery of D-Peptide Inhibitors that Target the Gp41 Coiled-Coil Pocket

Eckert, D.M.Malashkevich, V.N.Hong, L.H.Carr, P.A.Kim, P.S.

(1999) Cell 99: 103-105

  • DOI: https://doi.org/10.1016/s0092-8674(00)80066-5
  • Primary Citation Related Structures: 
    1CZQ, 2Q3I, 2Q5U, 2Q7C

  • PubMed Abstract: 

    The HIV-1 gp41 protein promotes viral entry by mediating the fusion of viral and cellular membranes. A prominent pocket on the surface of a central trimeric coiled coil within gp41 was previously identified as a potential target for drugs that inhibit HIV-1 entry. We designed a peptide, IQN17, which properly presents this pocket. Utilizing IQN17 and mirror-image phage display, we identified cyclic, D-peptide inhibitors of HIV-1 infection that share a sequence motif. A 1.5 A cocrystal structure of IQN17 in complex with a D-peptide, and NMR studies, show that conserved residues of these inhibitors make intimate contact with the gp41 pocket. Our studies validate the pocket per se as a target for drug development. IQN17 and these D-peptide inhibitors are likely to be useful for development and identification of a new class of orally bioavailable anti-HIV drugs.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA.

Macromolecule Content 

  • Total Structure Weight: 7.27 kDa 
  • Atom Count: 664 
  • Modeled Residue Count: 63 
  • Deposited Residue Count: 63 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI46N/AMutation(s): 0 
UniProt
Find proteins for A3F986 (Human immunodeficiency virus type 1)
Explore A3F986 
Go to UniProtKB:  A3F986
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3F986
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
D-peptideB [auth D]17N/AMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.258 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.702α = 90
b = 50.702β = 90
c = 67.858γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-11-13
    Changes: Structure summary