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9vg3

SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state

Method: X-RAY DIFFRACTION D_max: 66.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vg3
deposition_date	2025-06-12
title	SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state
keywords	deacetylase, 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	21.19 Å
rg_electron	19.99 Å
i0	18555300.00
molecular_weight	33271.0 kDa
excluded_volume	41919 Å³
envelope_volume	49173 Å³
shell_volume	20802 Å³
envelope_diameter	67.8 Å
shell_rg	26.21 Å
envelope_rg	20.10 Å
shape_rg	19.99 Å
total_rg	20.86 Å
total_atoms	2335
n_residues	299
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	66.7 Å
rg_real	21.14 Å
rg_real_error	0.29 Å
i0_real	1.8560e+07
i0_real_error	2.1480e+05
rg_reciprocal	21.15 Å
i0_reciprocal	18560000.0000
total_estimate	0.9014
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.5 Å
skewness	0.294
kurtosis	-0.370
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	3188000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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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	33961.2 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	2409

RLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

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	713.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

PRKQLA

Entity 3 non-polymer

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

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	54

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6. Citations (1)

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length_a	35.508 Å
length_b	72.528 Å
length_c	53.921 Å
angle_alpha	90.00 °
angle_beta	95.27 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.150 Å
resolution_low	53.751 Å
r_factor	—
r_work	0.1963
r_free	0.2511

fit	/app/data/saxs_computation/vg/9vg3/9vg3.fit
pddf	/app/data/pr_computation/vg/9vg3/9vg3.pr.out
profile	/app/data/saxs_computation/vg/9vg3/9vg3.dat

SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state

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)