6VQS

HIV Integrase Core domain (IN) in complex with [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid

• PDB DOI: https://doi.org/10.2210/pdb6VQS/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-05 Released: 2021-02-10 
• Deposition Author(s): Gorman, M.A., Parker, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.269 
• R-Value Work: 0.209 
• R-Value Observed: 0.215 

Literature

HIV Integrase Core domain (IN) in complex with [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid

Gorman, M.A., Parker, M.W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 18.91 kDa 
• Atom Count: 1,101 
• Modelled Residue Count: 136 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	163	Human immunodeficiency virus 1	Mutation(s): 0  EC: 2.7.7
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R7J (Subject of Investigation/LOI)	I [auth A]	[5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid C16 H11 F O3 ZIFXDKDCUJZEBV-UHFFFAOYSA-N
IOD	E [auth A], F [auth A], G [auth A], H [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.269 
• R-Value Work: 0.209 
• R-Value Observed: 0.215 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.158	α = 90
b = 46.158	β = 90
c = 138.373	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Gorman, M.A., Parker, M.W.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references