Human mitochondrial ClpP in complex with LZL25

Method: X-RAY DIFFRACTION D_max: 104.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9was
deposition_date	2025-08-12
last_revision	2026-04-22
title	Human mitochondrial ClpP in complex with LZL25
keywords	ClpP, Agonist, RECOMBINATION; RECOMBINATION
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	36.09 Å
rg_electron	35.22 Å
i0	594556000.00
molecular_weight	133300.0 kDa
excluded_volume	129510 Å³
envelope_volume	234650 Å³
shell_volume	53288 Å³
envelope_diameter	104.4 Å
shell_rg	44.34 Å
envelope_rg	33.90 Å
shape_rg	35.20 Å
total_rg	35.71 Å
total_atoms	10048
n_residues	1265
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	104.6 Å
rg_real	35.85 Å
rg_real_error	0.58 Å
i0_real	5.9460e+08
i0_real_error	9.2030e+06
rg_reciprocal	36.01 Å
i0_reciprocal	594600000.0000
total_estimate	0.9051
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	54.7 Å
skewness	-0.039
kurtosis	-0.802
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	82290000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.856

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	143.173 Å
length_b	151.847 Å
length_c	104.553 Å
angle_alpha	90.00 °
angle_beta	118.46 °
angle_gamma	90.00 °
z_pdb	28

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	3.519 Å
resolution_low	83.779 Å
r_factor	0.1837
r_work	0.1779
r_free	0.2472

description	ATP-dependent Clp protease proteolytic subunit, mitochondrial
formula_weight	21449.0 kDa
ec_number	3.4.21.92
src_method	man
entity_count	7

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G
atom_count	10108

Human mitochondrial ClpP in complex with LZL25

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

description	(3~{R})-7-[(4-fluorophenyl)methyl]-3-(2-methoxyethoxymethyl)-2-[[4-(trifluoromethyl)phenyl]methyl]-3,4-dihydroisoquinolin-1-one
formula_weight	501.5 kDa
src_method	syn
entity_count	7

fit	/app/data/saxs_computation/wa/9was/9was.fit
pddf	/app/data/pr_computation/wa/9was/9was.pr.out
profile	/app/data/saxs_computation/wa/9was/9was.dat