8BUV

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3

Singer, M.R.Cherepanov, P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase
A, B, C, D
233Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: gag-pol
EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
723 (Subject of Investigation/LOI)
Query on 723

Download Ideal Coordinates CCD File 
J [auth B],
N [auth D]
(6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid
C17 H12 Cl N O3
SHDUUQWYFNJIAG-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
I [auth B]
K [auth C]
F [auth B],
G [auth B],
H [auth B],
I [auth B],
K [auth C],
M [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth B],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.84α = 90
b = 65.16β = 99.9
c = 69.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001061
Medical Research Council (MRC, United Kingdom)United KingdomFC001061
Wellcome TrustUnited KingdomFC001061
The Francis Crick InstituteUnited KingdomFC001061

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release