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9qdw

Crystal structure of human PLA2G5 in complex with a SMOL inhibitor (compound 1)

Method: X-RAY DIFFRACTION D_max: 60.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdw
deposition_date	2025-03-07
last_revision	2026-03-18
title	Crystal structure of human PLA2G5 in complex with a SMOL inhibitor (compound 1)
keywords	Inhibitor complex Secreted phospholipase Lipid metabolism Drug discovery, HYDROLASE; HYDROLASE
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	19.24 Å
rg_electron	18.49 Å
i0	26097900.00
molecular_weight	26183.0 kDa
excluded_volume	25234 Å³
envelope_volume	40374 Å³
shell_volume	18301 Å³
envelope_diameter	60.2 Å
shell_rg	24.64 Å
envelope_rg	18.68 Å
shape_rg	18.53 Å
total_rg	19.06 Å
total_atoms	1953
n_residues	238
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	60.1 Å
rg_real	19.14 Å
rg_real_error	0.24 Å
i0_real	2.6100e+07
i0_real_error	2.7890e+05
rg_reciprocal	19.15 Å
i0_reciprocal	26100000.0000
total_estimate	0.9087
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.152
kurtosis	-0.516
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	5153000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Phospholipase A2 group V
formula_weight	13752.8 kDa
ec_number	3.1.1.4
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	1995

GSGLLDLKSMIEKVTGKNALTNYGFYGCYCGWGGRGTPKDGTDWCCWAHDHCYGRLEEKGCNIRTQSYKYRFAWGVVTCEPGPFCHVNLCACDRKLVYCLKRNLRSYNPQYQYFPNILCS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	4-[4-(trifluoromethyl)phenoxy]piperidine-1-carboxamide
formula_weight	288.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	42

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6. Citations (1)

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length_a	52.990 Å
length_b	67.290 Å
length_c	68.320 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	—

resolution	2.490 Å
resolution_low	30.460 Å
r_factor	0.2624
r_work	0.2596
r_free	0.3197

fit	/app/data/saxs_computation/qd/9qdw/9qdw.fit
pddf	/app/data/pr_computation/qd/9qdw/9qdw.pr.out
profile	/app/data/saxs_computation/qd/9qdw/9qdw.dat