SAXSdb — 9yid

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1. Structure Basics

entry_id	9yid
deposition_date	2025-10-01
title	AM12-352 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP
keywords	HIV-1, Envelope protein, Vaccine, Immunogen, Antibody, bNAb, Viral Protein, 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	50.03 Å
rg_electron	49.66 Å
i0	1296560000.00
molecular_weight	294430.0 kDa
excluded_volume	366300 Å³
envelope_volume	548000 Å³
shell_volume	91020 Å³
envelope_diameter	160.5 Å
shell_rg	54.65 Å
envelope_rg	48.65 Å
shape_rg	49.70 Å
total_rg	49.71 Å
total_atoms	20652
n_residues	2343
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	156.3 Å
rg_real	49.83 Å
rg_real_error	1.22 Å
i0_real	1.2970e+09
i0_real_error	2.3110e+07
rg_reciprocal	50.18 Å
i0_reciprocal	1297000000.0000
total_estimate	0.8858
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.6 Å
skewness	0.079
kurtosis	-0.512
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	80160000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.783

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Transmembrane protein gp41
formula_weight	17134.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,A
atom_count	20652

AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

description	Envelope glycoprotein gp120
formula_weight	53927.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,G,E

NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYTPNLTNDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKNKTFNGTGPCPNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGNVSKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 polymer

description	AM12-352 Fab heavy chain
formula_weight	14454.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,J,M

VQLQQWGEGRVQPSETLSLPCAVYGGSISDYYWSWIRQPPGEGLEWIAHVDPISPTIDYYNPSFKNRITISKDTSKNQFSLKLRSVTAADTAVYYCARAGPLRYYGPWNNQRRFDFWGPGVLVTVSS

Source

organism	Macaca mulatta
common_name	Rhesus monkey
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 4 polymer

description	AM12-352 Fab light chain
formula_weight	12338.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	K,L,N

DVVMTQSPLSLSITPGQPASISCRFSQSLVHSDGNTYLSWYQQKPGQPPRLLIYKVSNRDSGVPDRFSGSGAGTDFTLKISRLEAEDVGVYYCGQATHWPWTFGQGTKVEIK

Source

organism	Macaca mulatta
common_name	Rhesus monkey
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 5 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	30

Entity 6 branched

description	;alpha-D-mannopyranose-(1-3)-[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	3

Entity 7 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[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	1073.0 kDa
src_method	man
entity_count	3

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	30

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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	4.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.50 Å
resolution_method	—
num_particles	54994

fit	/app/data/saxs_computation/yi/9yid/9yid.fit
pddf	/app/data/pr_computation/yi/9yid/9yid.pr.out
profile	/app/data/saxs_computation/yi/9yid/9yid.dat

AM12-352 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP

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 (8)

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 branched

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)