1A5V

ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND MN CATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor.

Lubkowski, J.Yang, F.Alexandratos, J.Wlodawer, A.Zhao, H.Burke Jr., T.R.Neamati, N.Pommier, Y.Merkel, G.Skalka, A.M.

(1998) Proc.Natl.Acad.Sci.USA 95: 4831-4836

  • Primary Citation of Related Structures:  1A5W, 1A5X

  • PubMed Abstract: 
  • The x-ray structures of an inhibitor complex of the catalytic core domain of avian sarcoma virus integrase (ASV IN) were solved at 1.9- to 2.0-A resolution at two pH values, with and without Mn2+ cations. This inhibitor (Y-3), originally identified i ...

    The x-ray structures of an inhibitor complex of the catalytic core domain of avian sarcoma virus integrase (ASV IN) were solved at 1.9- to 2.0-A resolution at two pH values, with and without Mn2+ cations. This inhibitor (Y-3), originally identified in a screen for inhibitors of the catalytic activity of HIV type 1 integrase (HIV-1 IN), was found in the present study to be active against ASV IN as well as HIV-1 IN. The Y-3 molecule is located in close proximity to the enzyme active site, interacts with the flexible loop, alters loop conformation, and affects the conformations of active site residues. As crystallized, a Y-3 molecule stacks against its symmetry-related mate. Preincubation of IN with metal cations does not prevent inhibition, and Y-3 binding does not prevent binding of divalent cations to IN. Three compounds chemically related to Y-3 also were investigated, but no binding was observed in the crystals. Our results identify the structural elements of the inhibitor that likely determine its binding properties.


    Organizational Affiliation

    Macromolecular Structure Laboratory, Advanced BioScience Laboratories-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTEGRASE
A
158Rous sarcoma virus (strain Schmidt-Ruppin B)Gene Names: gag-pro-pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for O92956 (Rous sarcoma virus (strain Schmidt-Ruppin B))
Go to UniProtKB:  O92956
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Y3
Query on Y3

Download SDF File 
Download CCD File 
A
4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID
C12 H11 N O8 S2
DACUJXBUANTBKE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y3IC50: 800000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.152 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.444α = 90.00
b = 66.444β = 90.00
c = 81.065γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance