Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 35.89 kDa 
• Atom Count: 2840 
• Modelled Residue Count: 296 
• Deposited Residue Count: 326 
• Unique protein chains: 1

3L3U

Crystal structure of the HIV-1 integrase core domain to 1.4A

• PDB DOI: 10.2210/pdb3L3U/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-12-17 Released: 2010-03-31 
• Deposition Author(s): Wielens, J., Chalmers, D.K., Scanlon, M.J., Parker, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site.

Wielens, J., Headey, S.J., Jeevarajah, D., Rhodes, D.I., Deadman, J., Chalmers, D.K., Scanlon, M.J., Parker, M.W.

(2010) FEBS Lett 584: 1455-1462

• PubMed: 20227411 
• DOI: 10.1016/j.febslet.2010.03.016
• Primary Citation of Related Structures:  
  3L3U, 3L3V


• PubMed Abstract: 
  

HIV integrase (IN) is an essential enzyme in HIV replication and an important target for drug design. IN has been shown to interact with a number of cellular and viral proteins during the integration process. Disruption of these important interactions could provide a mechanism for allosteric inhibition of IN. We present the highest resolution crystal structure of the IN core domain to date. We also present a crystal structure of the IN core domain in complex with sucrose which is bound at the dimer interface in a region that has previously been reported to bind integrase inhibitors.

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Organizational Affiliation: 

Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POL polyprotein	A, B	163	Human immunodeficiency virus 1	Mutation(s): 4  Gene Names: pol EC: 2.7.7.49 (UniProt), 3.1.13.2 (UniProt), 3.1.26.13 (UniProt)
UniProt
Find proteins for Q72498 (Human immunodeficiency virus 1) Explore Q72498  Go to UniProtKB:  Q72498

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.55	α = 90
b = 62.434	β = 90
c = 81.127	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-17 
• Released Date: 2010-03-31 
Deposition Author(s): Wielens, J., Chalmers, D.K., Scanlon, M.J., Parker, M.W.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-12
  Changes: Database references
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations