PARP9 Macro Domain 2 in complex with NAD+

Method: X-RAY DIFFRACTION D_max: 73.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qyh
deposition_date	2025-04-17
last_revision	2025-05-28
title	PARP9 Macro Domain 2 in complex with NAD+
keywords	PARP9, MACRO DOMAIN, NAD+, TRANSFERASE; TRANSFERASE
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	22.13 Å
rg_electron	21.19 Å
i0	28356300.00
molecular_weight	42039.0 kDa
excluded_volume	53153 Å³
envelope_volume	61150 Å³
shell_volume	23816 Å³
envelope_diameter	78.5 Å
shell_rg	28.09 Å
envelope_rg	21.55 Å
shape_rg	21.17 Å
total_rg	22.12 Å
total_atoms	2950
n_residues	360
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	73.4 Å
rg_real	22.08 Å
rg_real_error	0.50 Å
i0_real	2.8360e+07
i0_real_error	3.9780e+05
rg_reciprocal	22.09 Å
i0_reciprocal	28360000.0000
total_estimate	0.8030
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	26.3 Å
skewness	0.319
kurtosis	-0.332
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	9485000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	53.428 Å
length_b	73.827 Å
length_c	58.465 Å
angle_alpha	90.00 °
angle_beta	116.90 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.500 Å
resolution_low	52.190 Å
r_factor	0.2023
r_work	0.1973
r_free	0.2460

description	Protein mono-ADP-ribosyltransferase PARP9
formula_weight	22232.9 kDa
ec_number	2.4.2.-
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	2963

PARP9 Macro Domain 2 in complex with 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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

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

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

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	13

fit	/app/data/saxs_computation/qy/9qyh/9qyh.fit
pddf	/app/data/pr_computation/qy/9qyh/9qyh.pr.out
profile	/app/data/saxs_computation/qy/9qyh/9qyh.dat