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9v7w

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3

Method: X-RAY DIFFRACTION D_max: 68.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v7w
deposition_date	2025-05-28
title	SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3
keywords	Deacylase, 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	21.11 Å
rg_electron	20.00 Å
i0	22529600.00
molecular_weight	36520.0 kDa
excluded_volume	45869 Å³
envelope_volume	52497 Å³
shell_volume	21831 Å³
envelope_diameter	70.1 Å
shell_rg	26.73 Å
envelope_rg	20.36 Å
shape_rg	19.97 Å
total_rg	20.99 Å
total_atoms	2554
n_residues	308
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	68.1 Å
rg_real	21.05 Å
rg_real_error	0.36 Å
i0_real	2.2530e+07
i0_real_error	2.8300e+05
rg_reciprocal	21.06 Å
i0_reciprocal	22530000.0000
total_estimate	0.8896
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.301
kurtosis	-0.312
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	3657000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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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	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	2732

SLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source

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

Entity 2 polymer

description	PRO-ARG-LYS-GLN-LEU-ALA
formula_weight	713.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

PRKQLA

Entity 3 non-polymer

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

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

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

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	90

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6. Citations (1)

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length_a	37.760 Å
length_b	76.570 Å
length_c	55.940 Å
angle_alpha	90.00 °
angle_beta	97.88 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.860 Å
resolution_low	44.930 Å
r_factor	—
r_work	0.1858
r_free	0.2314

fit	/app/data/saxs_computation/v7/9v7w/9v7w.fit
pddf	/app/data/pr_computation/v7/9v7w/9v7w.pr.out
profile	/app/data/saxs_computation/v7/9v7w/9v7w.dat

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3

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)