SAXSdb — 9v2l

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1. Structure Basics

entry_id	9v2l
deposition_date	2025-05-20
title	Complex structure of 2014-422 spike RBD bound to human DPP4
keywords	2014-422 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	42.88 Å
rg_electron	42.61 Å
i0	543538000.00
molecular_weight	193370.0 kDa
excluded_volume	241970 Å³
envelope_volume	329060 Å³
shell_volume	63858 Å³
envelope_diameter	142.7 Å
shell_rg	48.23 Å
envelope_rg	42.24 Å
shape_rg	42.54 Å
total_rg	43.11 Å
total_atoms	13652
n_residues	1657
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	139.4 Å
rg_real	42.90 Å
rg_real_error	1.55 Å
i0_real	5.4350e+08
i0_real_error	1.0820e+07
rg_reciprocal	42.88 Å
i0_reciprocal	543500000.0000
total_estimate	0.8800
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.2 Å
skewness	0.306
kurtosis	-0.581
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	62310000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.763

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	24514.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	13652

EVHSRGQFIEQPNSVECDFTKLLSGTPPQVYNFNRLVFTNCNYNLTKLLSLFMVNEFSCDGISPDAIARGCYSSLTVDYFAYPLSMKSYMQPGSAGVISQYNYKQSFANPTCRIFATAPANLTITKPSSYSFISKCSRLTGDNSHIETPIVINPGEYSICKNFAPNGFSQDGDYFTRQLSQLEGGGILVGVGSVTPMTDTLQMGFIISVQYGTDTNSVCPMMD

Source

organism	Middle East respiratory syndrome-related coronavirus
ncbi_taxonomy_id	1335626
host_organism	Trichoplusia ni

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	B,C

RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
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	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	7

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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	3.00 Å
resolution_method	—
num_particles	591107

fit	/app/data/saxs_computation/v2/9v2l/9v2l.fit
pddf	/app/data/pr_computation/v2/9v2l/9v2l.pr.out
profile	/app/data/saxs_computation/v2/9v2l/9v2l.dat

Complex structure of 2014-422 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

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)