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9q0t

Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor NR05-01

Method: X-RAY DIFFRACTION D_max: 59.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q0t
deposition_date	2025-08-13
title	Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor NR05-01
keywords	HIV-1 Protease, wild-type, Protease-Inhibitor complex, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	18.11 Å
rg_electron	17.07 Å
i0	8258580.00
molecular_weight	22167.0 kDa
excluded_volume	28168 Å³
envelope_volume	31473 Å³
shell_volume	15734 Å³
envelope_diameter	57.4 Å
shell_rg	22.83 Å
envelope_rg	17.40 Å
shape_rg	17.02 Å
total_rg	18.16 Å
total_atoms	3145
n_residues	198
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	59.3 Å
rg_real	18.07 Å
rg_real_error	0.31 Å
i0_real	8.2590e+06
i0_real_error	9.8020e+04
rg_reciprocal	18.07 Å
i0_reciprocal	8259000.0000
total_estimate	0.8801
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.8 Å
skewness	0.326
kurtosis	-0.276
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	3523000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.967

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Protease
formula_weight	10831.8 kDa
ec_number	3.4.23.16
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3369

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	;(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-{[(1S)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate ;
formula_weight	624.7 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	125

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6. Citations (1)

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length_a	62.265 Å
length_b	62.265 Å
length_c	81.760 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61
int_tables_number	169
crystal_system	hexagonal

resolution	1.870 Å
resolution_low	53.920 Å
r_factor	0.2051
r_work	0.2030
r_free	0.2335

fit	/app/data/saxs_computation/q0/9q0t/9q0t.fit
pddf	/app/data/pr_computation/q0/9q0t/9q0t.pr.out
profile	/app/data/saxs_computation/q0/9q0t/9q0t.dat