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9uzh

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with L-742,001

Method: X-RAY DIFFRACTION D_max: 126.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uzh
deposition_date	2025-05-16
title	Crystal structure of Kasokero virus cap- snatching endonuclease in complex with L-742,001
keywords	cap-snatching endonuclease, HYDROLASE; HYDROLASE
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	36.12 Å
rg_electron	36.67 Å
i0	168522000.00
molecular_weight	69695.0 kDa
excluded_volume	67347 Å³
envelope_volume	123690 Å³
shell_volume	31834 Å³
envelope_diameter	132.3 Å
shell_rg	37.87 Å
envelope_rg	36.73 Å
shape_rg	36.66 Å
total_rg	36.75 Å
total_atoms	5272
n_residues	678
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	126.1 Å
rg_real	36.70 Å
rg_real_error	1.35 Å
i0_real	1.6850e+08
i0_real_error	3.3310e+06
rg_reciprocal	36.34 Å
i0_reciprocal	168500000.0000
total_estimate	0.7493
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	31.5 Å
skewness	0.646
kurtosis	-0.247
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	7601000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.623; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.468; Smooth: 0.399

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	34355.0 kDa
ec_number	2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5797

GPLGSKKPIALICAELYKPFQDLFAALPKDCSEECQTLFEDIRNSESHASAWSSALRIKGVAYEGFFSLTNSWRYIPEDLKPTLGMAIQTVFPDKFEKFLERTHLHPEYRDFTPDYLMCRSRIFKSDRLNRSNVAVSRGKDKGGKKKETTVNKDQDDDAQSAVLLSHKKRFPMPEIAVQEVSSVSAVVDRFKSKSSEKGRPIRQEESRPKTESMQEDIEVDELLIVEVGYQTDIEGKVISDIEKWKGVVNLMSHLGIKVNVLTCADNSQTPRTDWWIDEKYVRLLLNSISYLFKELLENS

Source

organism	Kasokero virus
ncbi_taxonomy_id	1712570
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	mAb 2E9 Fab heavy chain
formula_weight	24722.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EVKLEESGGGLVRPGGSRKLSCAASGFTFSSYGMQWVRQAPEKGLEWVAYISSGSRTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYYCATGYGGTWFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	mAb 2E9 Fab light chain
formula_weight	23971.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QIVLSQSPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	(2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid
formula_weight	413.9 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	525

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6. Citations (1)

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length_a	37.350 Å
length_b	80.340 Å
length_c	116.190 Å
angle_alpha	90.00 °
angle_beta	93.37 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.950 Å
resolution_low	27.660 Å
r_factor	0.1801
r_work	0.1783
r_free	0.2143

fit	/app/data/saxs_computation/uz/9uzh/9uzh.fit
pddf	/app/data/pr_computation/uz/9uzh/9uzh.pr.out
profile	/app/data/saxs_computation/uz/9uzh/9uzh.dat

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with L-742,001

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)