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9q5d

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

Method: X-RAY DIFFRACTION D_max: 58.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q5d
deposition_date	2025-08-20
title	Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor J02-37
keywords	HIV-1 Protease, wild-type HIV-1 Protease, Protease-Inhibitor complex, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex; VIRAL PROTEIN, 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	17.96 Å
rg_electron	17.02 Å
i0	7843280.00
molecular_weight	22003.0 kDa
excluded_volume	28166 Å³
envelope_volume	30898 Å³
shell_volume	15537 Å³
envelope_diameter	56.6 Å
shell_rg	22.78 Å
envelope_rg	17.33 Å
shape_rg	17.02 Å
total_rg	17.98 Å
total_atoms	3152
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	58.8 Å
rg_real	17.93 Å
rg_real_error	0.37 Å
i0_real	7.8430e+06
i0_real_error	1.0070e+05
rg_reciprocal	17.93 Å
i0_reciprocal	7843000.0000
total_estimate	0.8807
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.7 Å
skewness	0.329
kurtosis	-0.288
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	3392000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.990

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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	B,A
atom_count	3356

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-({4-[(1R)-1-hydroxyethyl]benzene-1-sulfonyl}[(2S)-2-methylbutyl]amino)butan-2-yl]carbamate ;
formula_weight	626.7 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 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	169

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6. Citations (1)

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length_a	62.533 Å
length_b	62.533 Å
length_c	82.178 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	1.940 Å
resolution_low	19.860 Å
r_factor	0.2184
r_work	0.2105
r_free	0.2435

fit	/app/data/saxs_computation/q5/9q5d/9q5d.fit
pddf	/app/data/pr_computation/q5/9q5d/9q5d.pr.out
profile	/app/data/saxs_computation/q5/9q5d/9q5d.dat