2Z2T

Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Intrahelical Salt-bridges in a-Helical Peptide Enhances its Binding to the Target: A New Design for HIV-1 Fusion Inhibitors

Nishikawa, H., Nakamura, S., Kodama, E., Ito, S., Kajiwara, K., Izumi, K., Sakagami, Y., Oishi, S., Ohkubo, T., Kobayashi, Y., Fujii, N., Matsuoka, M.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
gp41 fragment N36
A, B, C
38N/AMutation(s): 0 
UniProt
Find proteins for Q70626 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123))
Explore Q70626 
Go to UniProtKB:  Q70626
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70626
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion inhibitor peptide SC34EK
D, E, F
36N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NLE
Query on NLE
D, E, F
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.014α = 90
b = 105.014β = 90
c = 78.308γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection