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9s23

Crystal structure of human SIRT2 in complex with peptide triazole inhibitor OTDi1

Method: X-RAY DIFFRACTION D_max: 70.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s23
deposition_date	2025-07-21
title	Crystal structure of human SIRT2 in complex with peptide triazole inhibitor OTDi1
keywords	Sirtuins, Inhibitor, 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	20.91 Å
rg_electron	20.08 Å
i0	33715300.00
molecular_weight	30263.0 kDa
excluded_volume	29447 Å³
envelope_volume	47770 Å³
shell_volume	20285 Å³
envelope_diameter	72.7 Å
shell_rg	26.31 Å
envelope_rg	20.29 Å
shape_rg	20.04 Å
total_rg	20.79 Å
total_atoms	2285
n_residues	284
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	70.9 Å
rg_real	20.90 Å
rg_real_error	0.43 Å
i0_real	3.3720e+07
i0_real_error	4.4440e+05
rg_reciprocal	20.90 Å
i0_reciprocal	33720000.0000
total_estimate	0.8736
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.6 Å
skewness	0.369
kurtosis	-0.307
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	5146000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.980

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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-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	2325

GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	C

EALPKATGG

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	4-dodecyl-1-ethyl-1,2,3-triazole
formula_weight	265.4 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	34

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6. Citations (1)

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length_a	89.621 Å
length_b	89.621 Å
length_c	133.033 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.300 Å
resolution_low	53.410 Å
r_factor	0.2278
r_work	0.2262
r_free	0.2590

fit	/app/data/saxs_computation/s2/9s23/9s23.fit
pddf	/app/data/pr_computation/s2/9s23/9s23.pr.out
profile	/app/data/saxs_computation/s2/9s23/9s23.dat

Crystal structure of human SIRT2 in complex with peptide triazole inhibitor OTDi1

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)