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9q57

XZ440 integrase inhibitor bound to Wild-type HIV-1 intasome

Method: ELECTRON MICROSCOPY D_max: 102.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q57
deposition_date	2025-08-20
title	XZ440 integrase inhibitor bound to Wild-type HIV-1 intasome
keywords	viral protein, protein complex, integrase inhibitor, VIRAL PROTEIN-INHIBITOR-DNA complex; VIRAL PROTEIN/INHIBITOR/DNA
method	ELECTRON MICROSCOPY

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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	29.51 Å
rg_electron	29.27 Å
i0	102173000.00
molecular_weight	74780.0 kDa
excluded_volume	91467 Å³
envelope_volume	118640 Å³
shell_volume	34851 Å³
envelope_diameter	108.2 Å
shell_rg	35.28 Å
envelope_rg	29.89 Å
shape_rg	29.26 Å
total_rg	29.83 Å
total_atoms	5224
n_residues	608
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	102.6 Å
rg_real	29.56 Å
rg_real_error	0.81 Å
i0_real	1.0220e+08
i0_real_error	1.5710e+06
rg_reciprocal	29.54 Å
i0_reciprocal	102200000.0000
total_estimate	0.8632
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.2 Å
skewness	0.454
kurtosis	-0.028
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	11010000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.904

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Integrase
formula_weight	40149.9 kDa
ec_number	2.7.7.-,3.1.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,C,D,B
atom_count	5336

MATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKKGGGGGGGGGGGFLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED

Source

organism	HIV-1 06TG.HT008
ncbi_taxonomy_id	587638
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	;DNA (5'-D(APCPTPGPCPTPAPGPAPGPAPTPTPTPTPC)-3') ;
formula_weight	5795.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

ACTGCTAGAGATTTTCCCG

Entity 3 polymer

description	;DNA (5'-D(PGPAPAPAPAPTPCPTPCPTPAPGPCPA)-3') ;
formula_weight	5220.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

CGGGAAAATCTCTAGCA

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide
formula_weight	377.3 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	91

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.280 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.28 Å
resolution_method	—
num_particles	261868

fit	/app/data/saxs_computation/q5/9q57/9q57.fit
pddf	/app/data/pr_computation/q5/9q57/9q57.pr.out
profile	/app/data/saxs_computation/q5/9q57/9q57.dat

XZ440 integrase inhibitor bound to Wild-type HIV-1 intasome

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)