← Back to search

9rg8

Crystal structure of DNPH1 bound by compound 1.

Method: X-RAY DIFFRACTION D_max: 62.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rg8
deposition_date	2025-06-05
title	Crystal structure of DNPH1 bound by compound 1.
keywords	DNPH1, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	19.14 Å
rg_electron	18.30 Å
i0	24078800.00
molecular_weight	25078.0 kDa
excluded_volume	24219 Å³
envelope_volume	38450 Å³
shell_volume	17877 Å³
envelope_diameter	63.8 Å
shell_rg	24.17 Å
envelope_rg	18.48 Å
shape_rg	18.29 Å
total_rg	18.95 Å
total_atoms	1908
n_residues	236
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

▼

3. P(r) Analysis (GNOM)

dmax	62.7 Å
rg_real	19.12 Å
rg_real_error	0.33 Å
i0_real	2.4080e+07
i0_real_error	2.8900e+05
rg_reciprocal	19.12 Å
i0_reciprocal	24080000.0000
total_estimate	0.8633
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.6 Å
skewness	0.388
kurtosis	-0.200
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	6190000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.736

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	5-hydroxymethyl-dUMP N-hydrolase
formula_weight	17174.3 kDa
ec_number	3.2.2.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	1961

MRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLEENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-[1-methyl-5-[[1-[3-(pyrimidin-2-ylamino)phenyl]carbonylpiperidin-4-yl]amino]-1,2,4-triazol-3-yl]-1~{H}-indole-6-carbonitrile
formula_weight	518.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	53

▶

6. Citations (1)

▶

length_a	52.394 Å
length_b	52.394 Å
length_c	361.382 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.070 Å
resolution_low	20.770 Å
r_factor	0.2446
r_work	0.2419
r_free	0.2993

fit	/app/data/saxs_computation/rg/9rg8/9rg8.fit
pddf	/app/data/pr_computation/rg/9rg8/9rg8.pr.out
profile	/app/data/saxs_computation/rg/9rg8/9rg8.dat

Crystal structure of DNPH1 bound by compound 1.

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