SAXSdb — 9rdh

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1. Structure Basics

entry_id	9rdh
deposition_date	2025-06-02
title	Structure of A16/G9 in complex with A56/K2 at pH 5.5 (vaccinia virus)
keywords	poxvirus, viral fusion, vaccinia virus, mpox virus, 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	35.10 Å
rg_electron	34.47 Å
i0	161948000.00
molecular_weight	101920.0 kDa
excluded_volume	127470 Å³
envelope_volume	173090 Å³
shell_volume	43370 Å³
envelope_diameter	120.7 Å
shell_rg	39.70 Å
envelope_rg	34.19 Å
shape_rg	34.45 Å
total_rg	34.93 Å
total_atoms	7164
n_residues	870
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	116.6 Å
rg_real	35.23 Å
rg_real_error	0.85 Å
i0_real	1.6190e+08
i0_real_error	2.5400e+06
rg_reciprocal	35.16 Å
i0_reciprocal	161900000.0000
total_estimate	0.8671
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.3 Å
skewness	0.449
kurtosis	-0.377
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	25670000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.782

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Virion membrane protein OPG143
formula_weight	39111.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7164

RSAAAVTLNRIKIAPGIADIRDKYMELGFNYPEYNRAVKFAEESYTYYYETSPGEIKPKFCLIDGMSIDHCSSFIVPEFAKQYVLIHGEPCSSFKFRPGSLIYYQNEVTPEYIKDLKHATDYIASGQRCHFIKKDYLLGDSDSVAKCCSKTNTKHCPKIFNNNYKTEHCDDFMTGFCRNDPGNPNCLEWLRAKRKPAMSTYSDICSKHMDARYCSEFIRIIRPDYFTFGDTALYVFCNDHKGNRNCWCANYPKSNSGDKYLGPRVCWLHECTDESRDRKWLYYNQDVQRTRCKYVGGSGLVPRGSGGSGGSHHHHHHHHGGSGTGGLNDIFEAQKIEWHE

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Drosophila melanogaster

Entity 2 polymer

description	Entry-fusion complex protein OPG094
formula_weight	35601.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AGGVSVELPKRDPPPGVPTDEMLLNVDKMHDVIAPAKLLEYVHIGPLAKDKEDKVKKRYPEFRLVNTGPGGLSALLRQSYAGTAPNCCRTFQRTHYWKKDGKISDKYEEGAVLESCWPDVHDTGKCDVDLFDWCQGDTFDRNICHQWIGSAFNRADRTVEGQQSLINLYNKMQTLCSKDASVPICESFLHHLRAHNTEDSKEMIDYILRQQSADFKQKYMRCSYPTRDKLEESLKYAEPRECWDPECSNANVNFLLTRNYNNLGLCNIVRGSGLVPRGSLEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Drosophila melanogaster

Entity 3 polymer

description	Superinfection exclusion protein
formula_weight	46738.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

YRLQGFTNAGIVAYKNIQDDNIVFSPFGYSFSMFMSLLPASGNTRIELLKTMDLRKRDLGPAFTELISGLAKLKTSKYTYTDLTYQSFVDNTVSIKPSYYQQYHRFGLYRLNFRRDAVNKINSIVERRSGMSNVVDSNMLDNNTLWAIINTIYFKGIWQYPFDITKTRNASFTNKYGTKTVPMMNVVTKLQGNTITIDDEEYDMVRLPYKDANISMYLAIGDNMTHFTDSITAAKLDYWSFQLGNKVYNLKLPKFSIENKRDIKSIAEMMAPSMFNPDNASFKHMTRDPLYIYKMFQNAKIDVDEQGTVAEASTIMVATARSSPEKLEFNTPFVFIIRHDITGFILFMGKVESPGSGLVPRGSGSAGWSHPQFEKGGGSGGGSGGGSWSHPQFEKGTGGLNDIFEAQKIEWHE

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Drosophila melanogaster

Entity 4 polymer

description	Protein OPG185
formula_weight	15592.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

RSTPFPQTSKKIGDDATLSCNRNNTNDYVVMSAWYKEPNSIILLAAKSDVLYFDNYTKDKISYDSPYDDLVTTITIKSLTARDAGTYVCAFFMTSTTNDTDKVDYEEYSTELIVNTDSEGSGLVPRGSGSGHHHHHHHH

Source

organism	Vaccinia virus Western Reserve
ncbi_taxonomy_id	696871
host_organism	Drosophila melanogaster

Entity 5 branched

description	;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	1

Entity 6 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	1

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

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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	triclinic

resolution	4.00 Å
resolution_method	—
num_particles	65223

fit	/app/data/saxs_computation/rd/9rdh/9rdh.fit
pddf	/app/data/pr_computation/rd/9rdh/9rdh.pr.out
profile	/app/data/saxs_computation/rd/9rdh/9rdh.dat

Structure of A16/G9 in complex with A56/K2 at pH 5.5 (vaccinia virus)

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)