SAXSdb — 9y7n

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1. Structure Basics

entry_id	9y7n
deposition_date	2025-09-10
title	HCMV Protease in complex with Fab5 - Class 3
keywords	Cytomegalovirus, protease, antibody, complex, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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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	27.65 Å
rg_electron	26.51 Å
i0	44500200.00
molecular_weight	50698.0 kDa
excluded_volume	62940 Å³
envelope_volume	83575 Å³
shell_volume	26732 Å³
envelope_diameter	97.7 Å
shell_rg	33.15 Å
envelope_rg	26.58 Å
shape_rg	26.52 Å
total_rg	27.18 Å
total_atoms	7018
n_residues	482
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	95.3 Å
rg_real	27.76 Å
rg_real_error	0.74 Å
i0_real	4.4500e+07
i0_real_error	6.4350e+05
rg_reciprocal	27.73 Å
i0_reciprocal	44500000.0000
total_estimate	0.8693
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.1 Å
skewness	0.441
kurtosis	-0.213
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	8202000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.916; Smooth: 0.887

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Assemblin
formula_weight	29089.7 kDa
ec_number	3.4.21.97
mutation	A143V, A209V
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7018

MHHHHHHMTMDEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEVATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDVSGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA

Source

organism	Cytomegalovirus
ncbi_taxonomy_id	10358
host_organism	Escherichia coli BL21

Entity 2 polymer

description	Fab5 Heavy Chain
formula_weight	24943.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLVQSGGGLVQPGRSLRLSCTASGFTFGDYAMSWFRQAPGKGLEWVGFIRSKAYGGTTEYAASVKGRFTISRDDSKSIAYLQMNSLKTEDTALYYCVVYNYYNYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 3 polymer

description	Fab5 light chain
formula_weight	23970.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

LDVVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQALQTPITFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.690 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.69 Å
resolution_method	—
num_particles	487566

fit	/app/data/saxs_computation/y7/9y7n/9y7n.fit
pddf	/app/data/pr_computation/y7/9y7n/9y7n.pr.out
profile	/app/data/saxs_computation/y7/9y7n/9y7n.dat

HCMV Protease in complex with Fab5 - Class 3

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)