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9s22

Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole inhibitor LG023 and ADP-ribose

Method: X-RAY DIFFRACTION D_max: 69.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s22
deposition_date	2025-07-21
title	Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole inhibitor LG023 and ADP-ribose
keywords	Sirtuins, Inhibitor, Covalent adduct, Deacetylation, 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	20.64 Å
rg_electron	19.86 Å
i0	39501500.00
molecular_weight	32578.0 kDa
excluded_volume	31517 Å³
envelope_volume	50203 Å³
shell_volume	21140 Å³
envelope_diameter	70.8 Å
shell_rg	26.38 Å
envelope_rg	20.19 Å
shape_rg	19.84 Å
total_rg	20.53 Å
total_atoms	2451
n_residues	300
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	69.4 Å
rg_real	20.59 Å
rg_real_error	0.42 Å
i0_real	3.9500e+07
i0_real_error	4.9520e+05
rg_reciprocal	20.60 Å
i0_reciprocal	39500000.0000
total_estimate	0.8763
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.332
kurtosis	-0.292
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	6352000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	NAD-dependent protein deacetylase sirtuin-2
formula_weight	34416.7 kDa
ec_number	3.5.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2597

GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 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-[[3-[[2-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]-1,3-thiazol-5-yl]methyl]phenoxy]methyl]-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ;
formula_weight	1008.9 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	126

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6. Citations (1)

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length_a	102.614 Å
length_b	47.457 Å
length_c	74.795 Å
angle_alpha	90.00 °
angle_beta	108.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.950 Å
resolution_low	71.140 Å
r_factor	0.1797
r_work	0.1779
r_free	0.2143

fit	/app/data/saxs_computation/s2/9s22/9s22.fit
pddf	/app/data/pr_computation/s2/9s22/9s22.pr.out
profile	/app/data/saxs_computation/s2/9s22/9s22.dat

Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole inhibitor LG023 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