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9yry

Crystal structure of HIV-1 Protease WT (NL4-3) in Complex with NR02-73

Method: X-RAY DIFFRACTION D_max: 57.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yry
deposition_date	2025-10-17
title	Crystal structure of HIV-1 Protease WT (NL4-3) in Complex with NR02-73
keywords	;HIV-1, NL4-3 PROTEASE, DRUG RESISTANCE, PROTEASE-INHIBITOR Complex, wild-type HIV-1 Protease, 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	18.02 Å
rg_electron	17.02 Å
i0	8393480.00
molecular_weight	22340.0 kDa
excluded_volume	28434 Å³
envelope_volume	31457 Å³
shell_volume	15777 Å³
envelope_diameter	57.3 Å
shell_rg	22.64 Å
envelope_rg	17.29 Å
shape_rg	17.02 Å
total_rg	17.95 Å
total_atoms	3184
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	57.6 Å
rg_real	17.97 Å
rg_real_error	0.25 Å
i0_real	8.3930e+06
i0_real_error	9.9790e+04
rg_reciprocal	17.98 Å
i0_reciprocal	8394000.0000
total_estimate	0.8932
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.2 Å
skewness	0.296
kurtosis	-0.336
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	2713000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

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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	3383

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	;(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-3-hydroxy-4-{[(1S)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl][(2S)-2-methylbutyl]amino}-1-phenylbutan-2-yl]carbamate ;
formula_weight	602.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	175

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6. Citations (1)

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length_a	51.003 Å
length_b	58.285 Å
length_c	62.274 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.950 Å
resolution_low	23.600 Å
r_factor	0.1798
r_work	0.1779
r_free	0.2144

fit	/app/data/saxs_computation/yr/9yry/9yry.fit
pddf	/app/data/pr_computation/yr/9yry/9yry.pr.out
profile	/app/data/saxs_computation/yr/9yry/9yry.dat

Crystal structure of HIV-1 Protease WT (NL4-3) in Complex with NR02-73

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