SAXSdb — 9q9s

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1. Structure Basics

entry_id	9q9s
deposition_date	2025-02-26
title	HSV-2 prefusion glycoprotein B bound by Nb1_gbHSV
keywords	viral membrane fusion protein, glycoprotein B, Herpes simplex virus 2, nanobody complex, VIRAL PROTEIN; VIRAL PROTEIN
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	42.42 Å
rg_electron	41.85 Å
i0	780255000.00
molecular_weight	223790.0 kDa
excluded_volume	277680 Å³
envelope_volume	396110 Å³
shell_volume	76797 Å³
envelope_diameter	134.2 Å
shell_rg	48.66 Å
envelope_rg	41.14 Å
shape_rg	41.85 Å
total_rg	42.18 Å
total_atoms	15738
n_residues	1935
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	129.5 Å
rg_real	42.20 Å
rg_real_error	0.78 Å
i0_real	7.8030e+08
i0_real_error	1.2520e+07
rg_reciprocal	42.42 Å
i0_reciprocal	780400000.0000
total_estimate	0.8939
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.5 Å
skewness	0.106
kurtosis	-0.568
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	108000000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.780

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Nb1_gbHSV
formula_weight	12821.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	d,e,f
atom_count	15738

QVQLVESGGGSVQPGGSLRLSCAASASGRLSMSGALGWYRQVQGKSRELVATITDRSSTNYADSVKGRFTISIDDAENTMYLQMNSLKPEDTGVYYCNARWRGMNVWGKGTRVTVSSTS

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 2 polymer

description	Envelope glycoprotein B
formula_weight	104648.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C

MRGGGLICALVVGALVAAVASAAPAAPAAPRASGGVAATVAANGGPASRPPPVPSPATTKARKRKTKKPPKRPEATPPPDANATVAAGHATLRAHLREIKVENADAQFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNMETTAFHRDDHETDMELKPAKVATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATSPTTRNLLTTPKFTVAWDWVPKRPAVCTMTKWQEVDEMLRAEYGGSFRFSSDAISTTFTTNLTQYSLSRVDLGDCIGRDAREAIDRMFARKYNATHIKVGQPQYYLATGGFLIAYQPLLSNTLAELYVREYMREQDRKPRNATPAPLREAPSANASVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRIAVAWCELQNHELTLWNEARKLNPNAIASATVGRRVSARMLGDVMAVSTCVPVAPDNVIVQNSMRVSSRPGTCYSRPLVSFRYEDQGPLIEGQLGENNELRLTRDALEPCTVGHRRYFIFGGGYVYFEEYAYSHQLSRADVTTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIRADANAAMFAGLCAFFEGMGDLGRAVGKVVMGVVGGVVSAVSGVSSFMSNPFGALAVGLLVLAGLVAAFFAFRYVLQLQRNPMKALYPLTTKELKTSDPGGVGGEGEEGAEGGGFDEAKLAEAREMIRYMALVSAMERTEHKARKKGTSALLSSKVTNMVLRKRNKARYSPLHNEDEAGDEDELGTLEVLFQGPGGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Human herpesvirus 2 strain 333
ncbi_taxonomy_id	10313
host_organism	Homo sapiens

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	12

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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	2.70 Å
resolution_method	—
num_particles	158509

fit	/app/data/saxs_computation/q9/9q9s/9q9s.fit
pddf	/app/data/pr_computation/q9/9q9s/9q9s.pr.out
profile	/app/data/saxs_computation/q9/9q9s/9q9s.dat

HSV-2 prefusion glycoprotein B bound by Nb1_gbHSV

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 branched

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)