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9qpa

;APH(2'')-IVa with an inhibitor ;

Method: X-RAY DIFFRACTION D_max: 109.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpa
deposition_date	2025-03-26
last_revision	2026-02-11
title	;APH(2'')-IVa with an inhibitor ;
keywords	inhibitor, complex, enzyme, ANTIBIOTIC; ANTIBIOTIC
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	33.09 Å
rg_electron	33.22 Å
i0	144210000.00
molecular_weight	65455.0 kDa
excluded_volume	64189 Å³
envelope_volume	115070 Å³
shell_volume	30920 Å³
envelope_diameter	116.8 Å
shell_rg	37.13 Å
envelope_rg	32.75 Å
shape_rg	33.23 Å
total_rg	33.44 Å
total_atoms	5021
n_residues	594
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	109.3 Å
rg_real	33.44 Å
rg_real_error	1.00 Å
i0_real	1.4420e+08
i0_real_error	2.1670e+06
rg_reciprocal	33.30 Å
i0_reciprocal	144200000.0000
total_estimate	0.8293
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.483
kurtosis	-0.505
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	10870000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.752; Smooth: 0.655

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	APH(2'')-Id
formula_weight	37596.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	5054

MGSSHHHHHHSSGLVPRGSHMRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK

Source

organism	Enterococcus casseliflavus
ncbi_taxonomy_id	37734
host_organism	Escherichia coli

Entity 2 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	11

Entity 3 non-polymer

description	(2~{S})-3-[4-(5-chloranyl-1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,2,3-triazol-1-yl]propane-1,2-diol
formula_weight	293.7 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	33

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6. Citations (1)

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length_a	77.417 Å
length_b	64.313 Å
length_c	75.482 Å
angle_alpha	90.00 °
angle_beta	91.72 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.500 Å
resolution_low	41.730 Å
r_factor	0.2169
r_work	0.2152
r_free	0.2773

fit	/app/data/saxs_computation/qp/9qpa/9qpa.fit
pddf	/app/data/pr_computation/qp/9qpa/9qpa.pr.out
profile	/app/data/saxs_computation/qp/9qpa/9qpa.dat

;APH(2'')-IVa with an inhibitor ;

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