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9q8h

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative BDH 34019023

Method: X-RAY DIFFRACTION D_max: 76.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q8h
deposition_date	2025-02-24
last_revision	2025-04-02
title	SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative BDH 34019023
keywords	methyltransferase, complex, inhibitor, 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	23.68 Å
rg_electron	22.58 Å
i0	39399300.00
molecular_weight	48071.0 kDa
excluded_volume	59978 Å³
envelope_volume	71693 Å³
shell_volume	26225 Å³
envelope_diameter	79.8 Å
shell_rg	29.85 Å
envelope_rg	23.27 Å
shape_rg	22.52 Å
total_rg	23.61 Å
total_atoms	6659
n_residues	415
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	76.4 Å
rg_real	23.62 Å
rg_real_error	0.50 Å
i0_real	3.9400e+07
i0_real_error	5.3790e+05
rg_reciprocal	23.64 Å
i0_reciprocal	39400000.0000
total_estimate	0.8180
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.290
kurtosis	-0.350
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	6698000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	;2'-O-methyltransferase nsp16 ;
formula_weight	34150.1 kDa
ec_number	2.1.1.57
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7019

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNNENLYFQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Non-structural protein 10
formula_weight	14860.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	S-ADENOSYLMETHIONINE
formula_weight	398.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	17

Entity 5 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	9-[(3~{R},4~{R})-1-(3-azanylpropanoyl)-4-oxidanyl-pyrrolidin-3-yl]-1,3-dimethyl-purine-2,6-dione
formula_weight	336.3 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	1

Entity 9 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	322

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6. Citations (1)

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length_a	168.200 Å
length_b	168.200 Å
length_c	52.010 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	1.802 Å
resolution_low	48.560 Å
r_factor	0.1925
r_work	0.1930
r_free	0.2191

fit	/app/data/saxs_computation/q8/9q8h/9q8h.fit
pddf	/app/data/pr_computation/q8/9q8h/9q8h.pr.out
profile	/app/data/saxs_computation/q8/9q8h/9q8h.dat

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative BDH 34019023

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 (11)

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 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)