3O3Z

Complex of a chimeric alpha/beta-peptide based on the gp41 CHR domain bound to a gp41 NHR domain peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Broad Distribution of Energetically Important Contacts across an Extended Protein Interface.

Johnson, L.M.Horne, W.S.Gellman, S.H.

(2011) J.Am.Chem.Soc. 133: 10038-10041

  • DOI: 10.1021/ja203358t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Infection of cells by HIV depends upon profound structural rearrangements within the trimeric viral protein gp41. Critical to this process is the formation of a six-helix bundle in which a set of three N-terminal heptad repeat (NHR) helices assemble ...

    Infection of cells by HIV depends upon profound structural rearrangements within the trimeric viral protein gp41. Critical to this process is the formation of a six-helix bundle in which a set of three N-terminal heptad repeat (NHR) helices assemble to form a core displaying long grooves that provide docking sites for three C-terminal heptad repeat (CHR) helices. We report experiments designed to discriminate between two alternative hypotheses regarding the source of affinity between individual CHR helices and the complementary groove: (1) affinity is dominated by interactions of a small cluster of side chains at one end of the CHR helix; or (2) affinity depends upon interactions distributed across the long CHR helix. We have employed two complementary experimental designs, and results from both favor the latter hypothesis.


    Organizational Affiliation

    Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
A
38N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
chimeric alpha/beta peptide based on gp41 CHR domain sequence
B
40N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 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
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
B3E
Query on B3E
B
L-PEPTIDE LINKINGC6 H11 N O4GLU
NH2
Query on NH2
A, B
NON-POLYMERH2 N

--

B3T
Query on B3T
B
L-peptide linkingC5 H11 N O3

--

XPC
Query on XPC
B
peptide-likeC5 H10 N2 O2

--

XCP
Query on XCP
B
peptide-likeC6 H11 N O2

--

ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.241 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 85.804α = 90.00
b = 85.804β = 90.00
c = 85.804γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
MD2data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2011-11-23
    Type: Structure summary