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9s27

Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose

Method: X-RAY DIFFRACTION D_max: 65.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s27
deposition_date	2025-07-21
title	Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose
keywords	Sirtuins, Mechanistic Inhibitor, Deacetylation, Covalent adduct, 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	20.29 Å
rg_electron	19.40 Å
i0	32779400.00
molecular_weight	29684.0 kDa
excluded_volume	28806 Å³
envelope_volume	45856 Å³
shell_volume	19988 Å³
envelope_diameter	66.3 Å
shell_rg	25.66 Å
envelope_rg	19.56 Å
shape_rg	19.33 Å
total_rg	20.17 Å
total_atoms	2249
n_residues	279
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	65.9 Å
rg_real	20.26 Å
rg_real_error	0.30 Å
i0_real	3.2780e+07
i0_real_error	4.1930e+05
rg_reciprocal	20.27 Å
i0_reciprocal	32780000.0000
total_estimate	0.8867
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.6 Å
skewness	0.342
kurtosis	-0.296
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	4677000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	NAD-dependent protein deacetylase sirtuin-3, mitochondrial
formula_weight	31268.0 kDa
ec_number	3.5.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2513

GHMSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	TNFa-derived lysine triazole dodecyl inhibitor
formula_weight	843.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

EALPKATGG

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(R,R)-2,3-BUTANEDIOL
formula_weight	90.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	;[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-(5-dodecyl-3-propyl-1,2,3$l^{4}-triazacyclopenta-2,4-dien-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ;
formula_weight	821.8 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	228

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6. Citations (1)

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length_a	97.102 Å
length_b	97.102 Å
length_c	203.673 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	1.600 Å
resolution_low	77.730 Å
r_factor	0.1814
r_work	0.1807
r_free	0.1938

fit	/app/data/saxs_computation/s2/9s27/9s27.fit
pddf	/app/data/pr_computation/s2/9s27/9s27.pr.out
profile	/app/data/saxs_computation/s2/9s27/9s27.dat

Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)