← Back to search

9saj

Crystal structure of SARS-CoV-2 NSP14 in complex with compound 5

Method: X-RAY DIFFRACTION D_max: 99.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9saj
deposition_date	2025-08-07
title	Crystal structure of SARS-CoV-2 NSP14 in complex with compound 5
keywords	NSP14, SARS-CoV-2 NSP14, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.18 Å
rg_electron	31.47 Å
i0	306318000.00
molecular_weight	94081.0 kDa
excluded_volume	91122 Å³
envelope_volume	162790 Å³
shell_volume	42260 Å³
envelope_diameter	104.6 Å
shell_rg	39.26 Å
envelope_rg	31.13 Å
shape_rg	31.44 Å
total_rg	32.00 Å
total_atoms	7068
n_residues	884
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	99.4 Å
rg_real	32.00 Å
rg_real_error	0.59 Å
i0_real	3.0630e+08
i0_real_error	4.3630e+06
rg_reciprocal	32.08 Å
i0_reciprocal	306300000.0000
total_estimate	0.9093
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	42.6 Å
skewness	0.088
kurtosis	-0.644
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	29990000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.961

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59544.2 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7225

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFAVAGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTR

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	7

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	1-[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethyl]-3-ethyl-urea
formula_weight	397.5 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	122

▶

6. Citations (1)

▶

length_a	67.805 Å
length_b	102.363 Å
length_c	90.743 Å
angle_alpha	90.00 °
angle_beta	109.19 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.480 Å
resolution_low	65.710 Å
r_factor	0.2023
r_work	0.2014
r_free	0.2386

fit	/app/data/saxs_computation/sa/9saj/9saj.fit
pddf	/app/data/pr_computation/sa/9saj/9saj.pr.out
profile	/app/data/saxs_computation/sa/9saj/9saj.dat