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9pz1

Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor LR4-43

Method: X-RAY DIFFRACTION D_max: 58.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pz1
deposition_date	2025-08-08
title	Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor LR4-43
keywords	HIV, HIV-1, HIV-1 protease, protease inhibitor, peptide-like inhibitor, 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	18.05 Å
rg_electron	16.99 Å
i0	7764010.00
molecular_weight	21698.0 kDa
excluded_volume	27690 Å³
envelope_volume	30588 Å³
shell_volume	15421 Å³
envelope_diameter	56.9 Å
shell_rg	22.81 Å
envelope_rg	17.32 Å
shape_rg	16.94 Å
total_rg	18.15 Å
total_atoms	3087
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	58.2 Å
rg_real	18.02 Å
rg_real_error	0.28 Å
i0_real	7.7640e+06
i0_real_error	9.8520e+04
rg_reciprocal	18.02 Å
i0_reciprocal	7764000.0000
total_estimate	0.8883
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	19.7 Å
skewness	0.333
kurtosis	-0.282
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	2943000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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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	A,B
atom_count	3250

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	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-1-(3,5-difluorophenyl)-4-[(2-ethylbutyl){4-[(1S)-1-hydroxyethyl]benzene-1-sulfonyl}amino]-3-hydroxybutan-2-yl}carbamate ;
formula_weight	640.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	131

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6. Citations (1)

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length_a	62.525 Å
length_b	62.525 Å
length_c	82.151 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	1.800 Å
resolution_low	19.250 Å
r_factor	0.2155
r_work	0.2104
r_free	0.2531

fit	/app/data/saxs_computation/pz/9pz1/9pz1.fit
pddf	/app/data/pr_computation/pz/9pz1/9pz1.pr.out
profile	/app/data/saxs_computation/pz/9pz1/9pz1.dat

Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor LR4-43

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