SAXSdb — 9uy9

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1. Structure Basics

entry_id	9uy9
deposition_date	2025-05-15
title	Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5
keywords	rhLCV, gB, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	56.00 Å
rg_electron	55.90 Å
i0	845470000.00
molecular_weight	228080.0 kDa
excluded_volume	279030 Å³
envelope_volume	480810 Å³
shell_volume	76064 Å³
envelope_diameter	175.5 Å
shell_rg	52.19 Å
envelope_rg	55.54 Å
shape_rg	55.89 Å
total_rg	55.77 Å
total_atoms	16151
n_residues	2310
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	162.0 Å
rg_real	56.10 Å
rg_real_error	1.43 Å
i0_real	8.4550e+08
i0_real_error	1.6450e+07
rg_reciprocal	55.88 Å
i0_reciprocal	845200000.0000
total_estimate	0.8442
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.4 Å
skewness	0.281
kurtosis	-0.675
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	49360000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.996; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Macacine gammaherpesvirus 4 glycoprotein B
formula_weight	78052.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	16151

MTPRRKPSVVLLLAALVGCIWAQTTQQPAPPATTVQPAAARQKTNFPFRVCELSSHGDLFRFSSDIQCPSSGTQEKHTEGLLMVFKDNIIPYSFKVRSYTKIVTNTLVYNGHRADAVTNRHEEMFSVESHETDQMDSIYQCHNAVRMTKDGVERVYVDNDGTNITVNLRPTSGLANGVRRYASQTQVHDAPGRVEATYRTRTTVNCVVTDMMAKSNSPFNFFVTTVGQTAEMSPFYDGTNKETFNERAGSFHVRENYKIVDYDNRGTVPNGERRAFLDKGTYTLSWKLENRTAYCPLQHWKTFESTIATETVRSTHFVTQEGTSSFVTNMTVGMALPGAFKCIEDQVNKTMHEKYEALQDRYVKDQENITYFLTSGGLLLAWLPLTPRSLASVKNLTELTTAAPPFPSSPTPPTPSTASRSTAAAIVRRRRRQAEGNNTTPAPPKPATPAPGNSLGTLNNPATIQIQFAYDSLRRQINRMLGDLARAWCLEQKRQNMVLRELTKINPTTVMSGIYGRPVAAKRLGDVISVSQCVPVNQATVTLRKSMRVPGSESMCYSRPLVSFSFINDTKTYEGQLGTDNEIFLTKKMTEMCLASSQYYFQSGNEIHVYHDYQHFKTIELDGIATLQTFIALNTSLIENIDFASLELYSRDEQRASNVFDLEGIFREYNFQAQNIAGLRKDLDNAVSHHHHHH

Source

organism	Macacine gammaherpesvirus 4
ncbi_taxonomy_id	45455
host_organism	Homo sapiens

Entity 2 polymer

description	Fab5 H chain
formula_weight	24199.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,I,J

QVQLQQPGAELVRPGASVKLSCKASGFTFTSYWINWVKQRPGQGLEWIGNIFPSDSYTNYNQKFKDKATLTVDKSSSTAYMLLSSPTSEDSAVYYCTRGGYRYDSDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVGSHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	Fab5 L chain
formula_weight	23261.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,M,N

QIVLTQSPAIMSASPGEKVTMTCSASSSVTYMYWYQQKPGSSPRLLIYDTSNLASGVPVRFSGSGSGTSYSLTISRMEAEDAATYYCQQWSSYPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

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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	3.50 Å
resolution_method	—
num_particles	91810

fit	/app/data/saxs_computation/uy/9uy9/9uy9.fit
pddf	/app/data/pr_computation/uy/9uy9/9uy9.pr.out
profile	/app/data/saxs_computation/uy/9uy9/9uy9.dat

Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5

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

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)