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9vh0

SIRT2-H187A structure in complex with H3K18myr peptide and native NAD

Method: X-RAY DIFFRACTION D_max: 101.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vh0
deposition_date	2025-06-16
title	SIRT2-H187A structure in complex with H3K18myr peptide and native NAD
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	29.96 Å
rg_electron	29.51 Å
i0	71900800.00
molecular_weight	66958.0 kDa
excluded_volume	83835 Å³
envelope_volume	103850 Å³
shell_volume	30678 Å³
envelope_diameter	107.0 Å
shell_rg	34.98 Å
envelope_rg	29.61 Å
shape_rg	29.53 Å
total_rg	29.95 Å
total_atoms	4691
n_residues	589
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	101.6 Å
rg_real	30.15 Å
rg_real_error	1.01 Å
i0_real	7.1900e+07
i0_real_error	1.2630e+06
rg_reciprocal	30.07 Å
i0_reciprocal	71900000.0000
total_estimate	0.8485
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	99.6 Å
skewness	0.514
kurtosis	-0.226
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	19330000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.800

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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	34193.5 kDa
ec_number	2.3.1.286,2.3.1.-
mutation	H187A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4743

QKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAAGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ

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	2

Polymer

type	polypeptide(L)
strand_id	C,D

APRKQL

Entity 3 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	40

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6. Citations (1)

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length_a	37.434 Å
length_b	48.130 Å
length_c	96.194 Å
angle_alpha	100.19 °
angle_beta	91.58 °
angle_gamma	112.17 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.410 Å
resolution_low	47.129 Å
r_factor	—
r_work	0.1976
r_free	0.2733

fit	/app/data/saxs_computation/vh/9vh0/9vh0.fit
pddf	/app/data/pr_computation/vh/9vh0/9vh0.pr.out
profile	/app/data/saxs_computation/vh/9vh0/9vh0.dat

SIRT2-H187A structure in complex with H3K18myr peptide and native NAD

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)