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9q13

Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR05-04

Method: X-RAY DIFFRACTION D_max: 59.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q13
deposition_date	2025-08-13
title	Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR05-04
keywords	HIV-1 Protease, wild-type HIV-1 Protease, 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	18.28 Å
rg_electron	17.19 Å
i0	8141930.00
molecular_weight	22007.0 kDa
excluded_volume	27998 Å³
envelope_volume	31280 Å³
shell_volume	15593 Å³
envelope_diameter	60.3 Å
shell_rg	22.90 Å
envelope_rg	17.58 Å
shape_rg	17.13 Å
total_rg	18.31 Å
total_atoms	3128
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	59.9 Å
rg_real	18.27 Å
rg_real_error	0.37 Å
i0_real	8.1420e+06
i0_real_error	9.3470e+04
rg_reciprocal	18.27 Å
i0_reciprocal	8142000.0000
total_estimate	0.6450
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	21.0 Å
skewness	0.363
kurtosis	-0.219
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	3087000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 0.330; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	B,A
atom_count	3320

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	;(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-{[(1R)-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 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	147

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6. Citations (1)

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length_a	62.363 Å
length_b	62.363 Å
length_c	82.305 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	1.720 Å
resolution_low	19.810 Å
r_factor	0.2167
r_work	0.2125
r_free	0.2374

fit	/app/data/saxs_computation/q1/9q13/9q13.fit
pddf	/app/data/pr_computation/q1/9q13/9q13.pr.out
profile	/app/data/saxs_computation/q1/9q13/9q13.dat

Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR05-04

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction