8T5B

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor EKC-110

• PDB DOI: https://doi.org/10.2210/pdb8T5B/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-12 Released: 2024-06-19 
• Deposition Author(s): Dinh, T., Kvaratskhelia, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.265 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

Literature

Understanding the resistance of Y99H and A128T mutations in HIV-1 Integrase against the effective anti-HIV drugs of STP0404 and BKC11

Dinh, T., Kvaratskhelia, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 48.18 kDa 
• Atom Count: 3,387 
• Modelled Residue Count: 411 
• Deposited Residue Count: 424 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	155	Human immunodeficiency virus 1	Mutation(s): 0  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	C, D	57	Human immunodeficiency virus 1	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QD6 (Subject of Investigation/LOI)	E [auth A], G [auth B]	(2S)-tert-butoxy{4-(4-chlorophenyl)-2,6-dimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid C26 H29 Cl N4 O3 LPFULWWLZWWADL-QHCPKHFHSA-N
MG	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.265 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.954	α = 90
b = 69.984	β = 100.73
c = 63.858	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Dinh, T., Kvaratskhelia, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI143649

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release