7LEH

HIV-1 Protease WT (NL4-3) in Complex with PU9 (LR2-80)

• PDB DOI: https://doi.org/10.2210/pdb7LEH/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-01-14 Released: 2022-01-26 
• Deposition Author(s): Lockbaum, G.J., Rusere, L.N., Henes, M., Kosovrasti, K., Lee, S.K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

HIV-1 Protease Inhibitors with a P1 Phosphonate Modification Maintain Potency against Drug Resistant Variants by Increased van der Waals Contacts with Flaps Residues

Lockbaum, G.J., Rusere, L.N., Henes, M., Kosovrasti, K., Lee, S.K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.53 kDa 
• Atom Count: 1,696 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A [auth B], B [auth A]	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: pol
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
XW4 (Subject of Investigation/LOI)	C [auth A]	diethyl [(4-{(2S,3R)-4-{[(2H-1,3-benzodioxol-5-yl)sulfonyl](2-ethylbutyl)amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate C35 H51 N2 O13 P S AVQWBQCLPXUUEF-VTHVVLAZSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.286	α = 90
b = 58.353	β = 90
c = 62.096	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Lockbaum, G.J., Rusere, L.N., Henes, M., Kosovrasti, K., Lee, S.K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM109767

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description