Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16441.15 
• Atom Count: 1161 
• Residue Count: 138 
• Unique protein chains: 1

2Q5U

Crystal structure of IQN17

• DOI: 10.2210/pdb2Q5U/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1


• Deposited: 2007-06-01 Released: 2007-06-12 
• Deposition Author(s): Malashkevich, V.N., Eckert, D.M., Hong, L.H., Kim, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.300 
• R-Value Work: 0.244 

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

• PubMed: 10520998 
• Primary Citation of Related Structures:  
  2Q7C, 2Q3I, 1CZQ


• 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.

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Related Citations: 

• Crystal Structure of GCN4-Piqi, a Trimeric Coiled-Coil with Buried Polar Residues.
  Eckert, D.M.,Malashkevich, V.N.,Kim, P.S.
  (1998) J.Mol.Biol. 284: 859
• Core structure of gp41 from the HIV envelope glycoprotein
  Chan, D.C.,Fass, D.,Berger, J.M.,Kim, P.S.
  (1997) Cell 89: 263




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fusion protein between yeast variant GCN4 and HIVgp41	A, B, C	46	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for A3F986 (Human immunodeficiency virus 1) Go to UniProtKB:  A3F986

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A, B, C	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.300 
• R-Value Work: 0.244 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 45.515	α = 90.00
b = 47.895	β = 90.00
c = 136.091	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
DENZO	data reduction
REFMAC	refinement
AMoRE	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-06-01 
• Released Date: 2007-06-12 
• Deposition Author(s): Malashkevich, V.N., Eckert, D.M., Hong, L.H., Kim, P.S.

Revision History 

• Version 1.0: 2007-06-12
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance