9Q5D | pdb_00009q5d

Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor J02-37

• PDB DOI: https://doi.org/10.2210/pdb9Q5D/pdb

• Classification: VIRAL PROTEIN, HYDROLASE/INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-08-20 Released: 2025-12-24 
• Deposition Author(s): Shaqra, A.M., Kaur, J., Schiffer, C.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.243 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Fluorinated HIV-1 Protease Inhibitors Containing Chiral Hydroxyethylbenzene and Indanol as P2' Ligands with Potent Activity Against Drug-Resistant Variants

Kaur, J., Spielvogel, E., Nageswara Rao, D., Rusere, L.N., Shaqra, A.M., Lockbaum, G.J., Maryam, A., Yilmaz, N.K., Swanstrom, R., 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: 22.49 kDa 
• Atom Count: 1,729 
• Modeled 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): 0  Gene Names: gag-pol EC: 3.4.23.16
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
A1COE (Subject of Investigation/LOI)	C [auth B]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-({4-[(1R)-1-hydroxyethyl]benzene-1-sulfonyl}[(2S)-2-methylbutyl]amino)butan-2-yl]carbamate C30 H40 F2 N2 O8 S TWPFEZUGJPMUHE-VCXVXRJXSA-N
PEG	D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.243 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.533	α = 90
b = 62.533	β = 90
c = 82.178	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Shaqra, A.M., Kaur, J., Schiffer, C.A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release