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9zvr

Crystal structure of HTLV-1 protease bound to darunavir at 2.1 angstroms with truncated flaps

Method: X-RAY DIFFRACTION D_max: 61.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zvr
deposition_date	2025-12-30
last_revision	2026-01-21
title	Crystal structure of HTLV-1 protease bound to darunavir at 2.1 angstroms with truncated flaps
keywords	;HTLV-1, PROTEASE, DRUG RESISTANCE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex ;; VIRAL PROTEIN/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	19.16 Å
rg_electron	18.35 Å
i0	17748800.00
molecular_weight	21898.0 kDa
excluded_volume	21513 Å³
envelope_volume	34806 Å³
shell_volume	16395 Å³
envelope_diameter	61.7 Å
shell_rg	23.86 Å
envelope_rg	18.54 Å
shape_rg	18.22 Å
total_rg	19.21 Å
total_atoms	1711
n_residues	212
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	61.1 Å
rg_real	19.17 Å
rg_real_error	0.46 Å
i0_real	1.7750e+07
i0_real_error	2.1780e+05
rg_reciprocal	19.17 Å
i0_reciprocal	17750000.0000
total_estimate	0.8200
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.2 Å
skewness	0.357
kurtosis	-0.406
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	3851000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	HTLV-1 Protease
formula_weight	12566.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	1962

PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP

Source

organism	Human T-cell leukemia virus type I
ncbi_taxonomy_id	11908
host_organism	Escherichia coli

Entity 2 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
formula_weight	547.7 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	94

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6. Citations (1)

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length_a	77.477 Å
length_b	77.477 Å
length_c	160.444 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 63 2 2
int_tables_number	182
crystal_system	hexagonal

resolution	2.100 Å
resolution_low	41.820 Å
r_factor	0.2179
r_work	0.2160
r_free	0.2529

fit	/app/data/saxs_computation/zv/9zvr/9zvr.fit
pddf	/app/data/pr_computation/zv/9zvr/9zvr.pr.out
profile	/app/data/saxs_computation/zv/9zvr/9zvr.dat