SAXSdb — 9y7l

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1. Structure Basics

entry_id	9y7l
deposition_date	2025-09-10
title	HCMV Protease in complex with Fab5 - Class 1
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	31.37 Å
rg_electron	29.98 Å
i0	60848000.00
molecular_weight	57712.0 kDa
excluded_volume	70605 Å³
envelope_volume	102220 Å³
shell_volume	29815 Å³
envelope_diameter	109.6 Å
shell_rg	35.24 Å
envelope_rg	30.69 Å
shape_rg	30.06 Å
total_rg	30.23 Å
total_atoms	7862
n_residues	585
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	106.6 Å
rg_real	31.68 Å
rg_real_error	0.86 Å
i0_real	6.0850e+07
i0_real_error	9.8470e+05
rg_reciprocal	31.55 Å
i0_reciprocal	60840000.0000
total_estimate	0.8351
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	31.4 Å
skewness	0.566
kurtosis	-0.215
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	11250000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.749; Smooth: 0.722

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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	7862

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	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	429127

fit	/app/data/saxs_computation/y7/9y7l/9y7l.fit
pddf	/app/data/pr_computation/y7/9y7l/9y7l.pr.out
profile	/app/data/saxs_computation/y7/9y7l/9y7l.dat

HCMV Protease in complex with Fab5 - Class 1

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)