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9v0h

Crystal structure of human SIRT5 in complex with inhibitor 0904

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v0h
deposition_date	2025-05-17
last_revision	2026-05-27
title	Crystal structure of human SIRT5 in complex with inhibitor 0904
keywords	Inhibitor, SIRT5, 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	27.20 Å
rg_electron	26.15 Å
i0	55617100.00
molecular_weight	56976.0 kDa
excluded_volume	70623 Å³
envelope_volume	85806 Å³
shell_volume	27814 Å³
envelope_diameter	89.2 Å
shell_rg	32.90 Å
envelope_rg	25.92 Å
shape_rg	26.02 Å
total_rg	27.22 Å
total_atoms	7838
n_residues	525
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	85.0 Å
rg_real	27.14 Å
rg_real_error	0.58 Å
i0_real	5.5620e+07
i0_real_error	8.3020e+05
rg_reciprocal	27.16 Å
i0_reciprocal	55620000.0000
total_estimate	0.9079
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.8 Å
skewness	0.202
kurtosis	-0.574
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	20670000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	NAD-dependent protein deacylase sirtuin-5, mitochondrial
formula_weight	29282.4 kDa
ec_number	2.3.1.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9442

ARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA

Source

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

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	;3-[[(~{E})-1-[3-[[2-(6-ethoxypyridin-3-yl)-5-[[(1~{R})-1-phenylpropyl]carbamoyl]pyrimidin-4-yl]amino]propylamino]-2-nitro-ethenyl]amino]propanoic acid ;
formula_weight	592.6 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	762

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6. Citations (1)

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length_a	42.370 Å
length_b	56.062 Å
length_c	66.125 Å
angle_alpha	108.55 °
angle_beta	104.66 °
angle_gamma	89.87 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.665 Å
resolution_low	48.490 Å
r_factor	0.2052
r_work	0.2040
r_free	0.2410

fit	/app/data/saxs_computation/v0/9v0h/9v0h.fit
pddf	/app/data/pr_computation/v0/9v0h/9v0h.pr.out
profile	/app/data/saxs_computation/v0/9v0h/9v0h.dat

Crystal structure of human SIRT5 in complex with inhibitor 0904

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