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9ykp

HIV-1 Protease WT (NL4-3) with Inhibitor NR01-141

Method: X-RAY DIFFRACTION D_max: 56.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ykp
deposition_date	2025-10-07
title	HIV-1 Protease WT (NL4-3) with Inhibitor NR01-141
keywords	;HIV, NL4-3 PROTEASE, DRUG RESISTANCE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, VIRAL PROTEIN, 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	18.08 Å
rg_electron	17.00 Å
i0	8551350.00
molecular_weight	22143.0 kDa
excluded_volume	27989 Å³
envelope_volume	31168 Å³
shell_volume	15680 Å³
envelope_diameter	57.4 Å
shell_rg	22.62 Å
envelope_rg	17.26 Å
shape_rg	17.00 Å
total_rg	17.91 Å
total_atoms	3114
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	56.9 Å
rg_real	18.03 Å
rg_real_error	0.30 Å
i0_real	8.5510e+06
i0_real_error	1.0180e+05
rg_reciprocal	18.03 Å
i0_reciprocal	8551000.0000
total_estimate	0.8970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.8 Å
skewness	0.292
kurtosis	-0.345
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	2589000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.984

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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	3280

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	5

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](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate ;
formula_weight	588.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	166

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6. Citations (1)

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length_a	51.029 Å
length_b	58.508 Å
length_c	62.116 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	1.960 Å
resolution_low	23.600 Å
r_factor	0.1830
r_work	0.1809
r_free	0.2267

fit	/app/data/saxs_computation/yk/9ykp/9ykp.fit
pddf	/app/data/pr_computation/yk/9ykp/9ykp.pr.out
profile	/app/data/saxs_computation/yk/9ykp/9ykp.dat

HIV-1 Protease WT (NL4-3) with Inhibitor NR01-141

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