SAXSdb — 9ugj

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1. Structure Basics

entry_id	9ugj
deposition_date	2025-04-12
title	Structure of SARM1 bound to SIR3-ADPR
keywords	NAD(+) hydrolase, cell death, apoptosis, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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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	41.33 Å
rg_electron	41.53 Å
i0	419371000.00
molecular_weight	112790.0 kDa
excluded_volume	109780 Å³
envelope_volume	207520 Å³
shell_volume	44023 Å³
envelope_diameter	147.1 Å
shell_rg	43.59 Å
envelope_rg	41.18 Å
shape_rg	41.51 Å
total_rg	41.64 Å
total_atoms	8542
n_residues	1106
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	141.7 Å
rg_real	41.66 Å
rg_real_error	1.47 Å
i0_real	4.1940e+08
i0_real_error	8.2360e+06
rg_reciprocal	41.33 Å
i0_reciprocal	419200000.0000
total_estimate	0.8198
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.0 Å
skewness	0.529
kurtosis	-0.404
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	15380000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.575

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	NAD(+) hydrolase SARM1
formula_weight	83940.8 kDa
ec_number	3.2.2.6,3.2.2.-
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	8542

MVLTLLLSAYKLCRFFAMSGPRPGAERLAVPGPDGGGGTGPWWAAGGRGPREVSPGAGTEVQDALERALPELQQALSALKQAGGARAVGAGLAEVFQLVEEAWLLPAVGREVAQGLCDAIRLDGGLDLLLRLLQAPELETRVQAARLLEQILVAENRDRVARIGLGVILNLAKEREPVELARSVAGILEHMFKHSEETCQRLVAAGGLDAVLYWCRRTDPALLRHCALALGNCALHGGQAVQRRMVEKRAAEWLFPLAFSKEDELLRLHACLAVAVLATNKEVEREVERSGTLALVEPLVASLDPGRFARCLVDASDTSQGRGPDDLQRLVPLLDSNRLEAQCIGAFYLCAEAAIKSLQGKTKVFSDIGAIQSLKRLVCYSTNGTKSALAKRALRLLGEEVPRPILPSVPSWKEAEVQTWLQCIGFSKYCESFREQQVDGDLLLRLTEEELQTDLGMKSGITRKRFFRELTELKTFANYSTCDRSNLADWLGSLDPRFRQYTYGLVSCGLDRSLLHRVSEQQLLEDCGIHLGVHRARILTAAREMLHSPLPCTGGKPSGDTPDVFISYRRNSGSQLASLLKVHLQLHGFSVFIDVEKLEAGKFEDKLIQSVMGARNFVLVLSPGALDKCMQDHDCKDWVHKEIVTALSCGKNIVPIIDGFEWPEPQVLPEDMQAVLTFNGIKWSHEYQEATIEKIIRFLQGRSSRDSSAGSDTSLEGAAPMGPTYPYDVPDYATRGTSRDYKDHDGDYKDHDIDYKDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	;[[(2~{S},3~{R},4~{S},5~{S})-5-(4-azanylimidazo[4,5-d]pyridazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-methyl-3-(2-oxidanylidene-3~{H}-1,3-benzoxazol-6-yl)pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ;
formula_weight	768.5 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.850 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.85 Å
resolution_method	—
num_particles	28854

fit	/app/data/saxs_computation/ug/9ugj/9ugj.fit
pddf	/app/data/pr_computation/ug/9ugj/9ugj.pr.out
profile	/app/data/saxs_computation/ug/9ugj/9ugj.dat

Structure of SARM1 bound to SIR3-ADPR

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)