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9th6

nsp14 of SARS-CoV-2 in complex with a camelid nanobody

Method: X-RAY DIFFRACTION D_max: 93.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9th6
deposition_date	2025-12-02
last_revision	2026-02-11
title	nsp14 of SARS-CoV-2 in complex with a camelid nanobody
keywords	Complex, Nuclease, VHH, nsp, SARS-CoV-2, 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	29.99 Å
rg_electron	29.23 Å
i0	67550400.00
molecular_weight	64193.0 kDa
excluded_volume	80016 Å³
envelope_volume	102770 Å³
shell_volume	29625 Å³
envelope_diameter	94.7 Å
shell_rg	36.03 Å
envelope_rg	29.19 Å
shape_rg	29.23 Å
total_rg	29.86 Å
total_atoms	8837
n_residues	573
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	93.0 Å
rg_real	29.96 Å
rg_real_error	0.59 Å
i0_real	6.7550e+07
i0_real_error	1.0340e+06
rg_reciprocal	29.97 Å
i0_reciprocal	67550000.0000
total_estimate	0.9046
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	28.1 Å
skewness	0.169
kurtosis	-0.788
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	9649000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.926

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	62264.0 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	9197

MGGSHHHHHHHHGSENLYFQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

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

Entity 2 polymer

description	vhh anti-nsp14 of SARS-CoV-2
formula_weight	14290.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MAQVQLVESGGGLVQPGGSLRLSCAASGRAFTMYAMGWFRQAPGEERAYIAGITWNGLSTYYADSVKGRFTISRDNAKNTVYLQMGSLKPEDTAVYYCAATRRSLTTATTDADAWGQGTQVTVSSGHHHHHH

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	120

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6. Citations (1)

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length_a	55.514 Å
length_b	80.801 Å
length_c	138.117 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.267 Å
resolution_low	69.740 Å
r_factor	0.2361
r_work	0.2333
r_free	0.2897

fit	/app/data/saxs_computation/th/9th6/9th6.fit
pddf	/app/data/pr_computation/th/9th6/9th6.pr.out
profile	/app/data/saxs_computation/th/9th6/9th6.dat

nsp14 of SARS-CoV-2 in complex with a camelid nanobody

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)