6W42 | pdb_00006w42

HIV Integrase core domain in complex with inhibitor 2-(5-methyl-2-(2-(thiophen-2-yl)ethynyl)-1-benzofuran-3-yl)acetic acid

• PDB DOI: https://doi.org/10.2210/pdb6W42/pdb

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


• Deposited: 2020-03-09 Released: 2021-03-10 
• Deposition Author(s): Gorman, M.A., Parker, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.259 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

HIV Integrase core domain in complex with inhibitor (5-methyl-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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19 kDa 
• Atom Count: 1,126 
• Modeled Residue Count: 139 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Integrase catalytic domain	A	165	Human immunodeficiency virus 1	Mutation(s): 0  EC: 2.7.7.49
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
SJY (Subject of Investigation/LOI)	H [auth A]	2-[5-methyl-2-(2-thiophen-2-ylethynyl)-1-benzofuran-3-yl]ethanoic acid C17 H12 O3 S IEIHBCBAJNGRHJ-UHFFFAOYSA-N
IOD	D [auth A], E [auth A], F [auth A], G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.259 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.18	α = 90
b = 46.18	β = 90
c = 139.43	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Gorman, M.A., Parker, M.W.

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary