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9vg0

SIRT2 structure in complex with H3K18myr peptide

Method: X-RAY DIFFRACTION D_max: 68.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vg0
deposition_date	2025-06-12
title	SIRT2 structure in complex with H3K18myr peptide
keywords	Deacylated, cell cycle regulation, Metabolic regulation, 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	21.00 Å
rg_electron	19.84 Å
i0	18165500.00
molecular_weight	32891.0 kDa
excluded_volume	41445 Å³
envelope_volume	48408 Å³
shell_volume	20582 Å³
envelope_diameter	70.8 Å
shell_rg	26.16 Å
envelope_rg	20.12 Å
shape_rg	19.83 Å
total_rg	20.74 Å
total_atoms	2306
n_residues	293
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	68.2 Å
rg_real	20.96 Å
rg_real_error	0.37 Å
i0_real	1.8170e+07
i0_real_error	2.2710e+05
rg_reciprocal	20.97 Å
i0_reciprocal	18170000.0000
total_estimate	0.6982
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.7 Å
skewness	0.328
kurtosis	-0.300
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	3231000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

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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	34692.0 kDa
ec_number	2.3.1.286,2.3.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2525

SLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source

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

Entity 2 polymer

description	Histone H3.1
formula_weight	784.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

APRKQLA

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	174

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6. Citations (1)

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length_a	36.152 Å
length_b	73.504 Å
length_c	55.731 Å
angle_alpha	90.00 °
angle_beta	94.09 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.610 Å
resolution_low	27.810 Å
r_factor	—
r_work	0.1883
r_free	0.2313

fit	/app/data/saxs_computation/vg/9vg0/9vg0.fit
pddf	/app/data/pr_computation/vg/9vg0/9vg0.pr.out
profile	/app/data/saxs_computation/vg/9vg0/9vg0.dat

SIRT2 structure in complex with H3K18myr peptide

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)