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9q5e

Hsa bound to Neu5Ac alpha2,3 Gal beta OMe

Method: X-RAY DIFFRACTION D_max: 82.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q5e
deposition_date	2025-08-20
last_revision	2025-11-26
title	Hsa bound to Neu5Ac alpha2,3 Gal beta OMe
keywords	Glycan binding protein, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
method	X-RAY DIFFRACTION

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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	23.67 Å
rg_electron	23.27 Å
i0	9943600.00
molecular_weight	22993.0 kDa
excluded_volume	28479 Å³
envelope_volume	34834 Å³
shell_volume	14247 Å³
envelope_diameter	83.1 Å
shell_rg	26.99 Å
envelope_rg	23.73 Å
shape_rg	23.22 Å
total_rg	23.92 Å
total_atoms	3179
n_residues	205
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	82.5 Å
rg_real	24.08 Å
rg_real_error	0.97 Å
i0_real	9.9440e+06
i0_real_error	1.4860e+05
rg_reciprocal	23.99 Å
i0_reciprocal	9943000.0000
total_estimate	0.7604
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	18.1 Å
skewness	0.608
kurtosis	-0.382
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	1595000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.545; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.271; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Streptococcal hemagglutinin
formula_weight	23092.4 kDa
mutation	D381E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3587

DTEAPQVKSGDYVVYRGESFEYYAEITDNSGQVNRVVIRNVEGGANSTYLSPNWVKYSTENLGRPGNATVQNPLRTRIFGEVPLNEIVNEKSYYTRYIVAWDPSGNATQMVDNANRNGLERFVLTVKSQNEKYDPAEPSVTYVNNLSNLSTSEREAVAAAVRAANPNIPPTAKITVSQNGTVTITYPDKSTDTIPANRVVKDLQISKSN

Source

organism	Streptococcus
ncbi_taxonomy_id	1301
host_organism	Escherichia coli

Entity 2 branched

description	N-acetyl-alpha-neuraminic acid-(2-3)-methyl beta-D-galactopyranoside
formula_weight	485.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	304

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6. Citations (1)

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length_a	45.302 Å
length_b	57.567 Å
length_c	75.685 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.290 Å
resolution_low	38.870 Å
r_factor	0.1626
r_work	0.1606
r_free	0.1910

fit	/app/data/saxs_computation/q5/9q5e/9q5e.fit
pddf	/app/data/pr_computation/q5/9q5e/9q5e.pr.out
profile	/app/data/saxs_computation/q5/9q5e/9q5e.dat