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9vem

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1

Method: X-RAY DIFFRACTION D_max: 66.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vem
deposition_date	2025-06-09
title	SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1
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	20.72 Å
rg_electron	19.54 Å
i0	20073300.00
molecular_weight	33827.0 kDa
excluded_volume	42239 Å³
envelope_volume	49229 Å³
shell_volume	21040 Å³
envelope_diameter	67.6 Å
shell_rg	26.17 Å
envelope_rg	19.87 Å
shape_rg	19.53 Å
total_rg	20.49 Å
total_atoms	2366
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	66.2 Å
rg_real	20.66 Å
rg_real_error	0.41 Å
i0_real	2.0070e+07
i0_real_error	2.9530e+05
rg_reciprocal	20.67 Å
i0_reciprocal	20070000.0000
total_estimate	0.8876
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.317
kurtosis	-0.255
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	3320000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	NAD-dependent protein deacetylase sirtuin-2
formula_weight	34404.7 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	2430

GSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

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

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	1

Entity 9 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	37.859 Å
length_b	76.409 Å
length_c	55.640 Å
angle_alpha	90.00 °
angle_beta	97.29 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.570 Å
resolution_low	55.251 Å
r_factor	—
r_work	0.1867
r_free	0.2642

fit	/app/data/saxs_computation/ve/9vem/9vem.fit
pddf	/app/data/pr_computation/ve/9vem/9vem.pr.out
profile	/app/data/saxs_computation/ve/9vem/9vem.dat

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1

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 (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)