SAXSdb — 9sak

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1. Structure Basics

entry_id	9sak
deposition_date	2025-08-07
title	Crystal structure of SARS-CoV-2 NSP14 in complex with compound 6
keywords	NSP14, SARS-CoV-2 NSP14, VIRAL PROTEIN; VIRAL PROTEIN
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	31.97 Å
rg_electron	31.24 Å
i0	290412000.00
molecular_weight	91694.0 kDa
excluded_volume	88900 Å³
envelope_volume	158320 Å³
shell_volume	41455 Å³
envelope_diameter	104.5 Å
shell_rg	38.94 Å
envelope_rg	30.88 Å
shape_rg	31.21 Å
total_rg	31.77 Å
total_atoms	6882
n_residues	873
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	98.2 Å
rg_real	31.78 Å
rg_real_error	0.57 Å
i0_real	2.9040e+08
i0_real_error	4.1750e+06
rg_reciprocal	31.86 Å
i0_reciprocal	290400000.0000
total_estimate	0.9091
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	43.2 Å
skewness	0.082
kurtosis	-0.644
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	29360000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.952

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59560.2 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7055

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFAVAGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTR

Source

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

Entity 2 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59576.2 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFAVAGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTR

Source

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

Entity 3 non-polymer

description	(2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-(naphthalen-2-ylsulfanylmethyl)oxolane-3,4-diol
formula_weight	409.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	7

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

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6. Citations (1)

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length_a	67.383 Å
length_b	102.050 Å
length_c	90.869 Å
angle_alpha	90.00 °
angle_beta	108.72 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.300 Å
resolution_low	44.840 Å
r_factor	0.2007
r_work	0.1995
r_free	0.2493

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

Crystal structure of SARS-CoV-2 NSP14 in complex with compound 6

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)