SAXSdb — 9v2p

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1. Structure Basics

entry_id	9v2p
deposition_date	2025-05-20
title	Complex structure of GX2012 spike RBD bound to human DPP4
keywords	GX2012 RBD, human DPP4, viral protein, hydrolase, VIRAL PROTEIN/HYDROLASE, VIRAL PROTEIN-HYDROLASE complex; VIRAL PROTEIN/HYDROLASE
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	43.09 Å
rg_electron	42.81 Å
i0	560510000.00
molecular_weight	196780.0 kDa
excluded_volume	246430 Å³
envelope_volume	338270 Å³
shell_volume	65360 Å³
envelope_diameter	145.6 Å
shell_rg	48.47 Å
envelope_rg	42.29 Å
shape_rg	42.74 Å
total_rg	43.30 Å
total_atoms	13891
n_residues	1663
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	142.3 Å
rg_real	43.11 Å
rg_real_error	1.54 Å
i0_real	5.6050e+08
i0_real_error	9.8880e+06
rg_reciprocal	43.09 Å
i0_reciprocal	560500000.0000
total_estimate	0.8811
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.2 Å
skewness	0.310
kurtosis	-0.556
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	67120000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.843

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Dipeptidyl peptidase 4 soluble form
formula_weight	84375.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13891

RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Spike glycoprotein
formula_weight	23031.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

TECDFSPMFKGVAPQVYNFKRLVFSNCNYNLTKLLSLFAVDEFSCNGISPDAIARGCYSTLTVDYFAYPLSMKSYIRPGSAGNIPLYNYKQSFAHPTCRVLASVPPNVTITKPEAYGYISKCSRLTGDYQHIETPLYINPGEYSICRDFAPLGFSEDGQVFKRTLTQFEGGGLLIGVGTRVPMTANLEMGFVISVQYGAGTDSVCPMLD

Source

organism	BtTp-BetaCoV/GX2012
ncbi_taxonomy_id	1503304
host_organism	Trichoplusia ni

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	11

Entity 4 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	2.40 Å
resolution_method	—
num_particles	447216

fit	/app/data/saxs_computation/v2/9v2p/9v2p.fit
pddf	/app/data/pr_computation/v2/9v2p/9v2p.pr.out
profile	/app/data/saxs_computation/v2/9v2p/9v2p.dat

Complex structure of GX2012 spike RBD bound to human DPP4

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)