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11zw

;Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody ;

Method: ELECTRON MICROSCOPY D_max: 108.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11zw
deposition_date	2026-03-21
title	;Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody ;
keywords	;porcine deltacoronavirus, minibinder, protein design, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, 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	33.70 Å
rg_electron	33.40 Å
i0	109184000.00
molecular_weight	83669.0 kDa
excluded_volume	104720 Å³
envelope_volume	141030 Å³
shell_volume	36446 Å³
envelope_diameter	114.2 Å
shell_rg	39.08 Å
envelope_rg	32.88 Å
shape_rg	33.38 Å
total_rg	33.93 Å
total_atoms	5900
n_residues	777
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	108.7 Å
rg_real	33.71 Å
rg_real_error	1.17 Å
i0_real	1.0920e+08
i0_real_error	2.0080e+06
rg_reciprocal	33.71 Å
i0_reciprocal	109200000.0000
total_estimate	0.9015
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.0 Å
skewness	0.281
kurtosis	-0.584
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	10590000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.929

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	PDCoV IL121_2014 receptor binding domain
formula_weight	19285.9 kDa
ec_number	3.1.3.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6116

MGILPSPGMPALLSLVSLLSVLLMGCVAETGTPELEVVQLNISAHMDFGEARLDSVTINGNTSYCVTKPYFRLETNFMCTGCTMNLRTDTCSFDLSAVNNGMSFSQFCLSTESGACEMKIIVTYVWNYLLRQRLYVTAVEGQTHTGGGSGLNDIFEAQKIEWHEGGSHHHHHHHH

Source

organism	Porcine deltacoronavirus
ncbi_taxonomy_id	1586324
host_organism	Homo sapiens

Entity 2 polymer

description	RBD minibinder 11
formula_weight	20905.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHHHHHHHHGGSLVPRGSGGSGLNDIFEAQKIEWHEGGSHMLTREEVQAIIDGHVIEVKYDSVEEFLEKYKGKISEETIELIEKLIELTSKDPKLSRLPLIFMQMLDMFIEIMKDLKDRGITSEEDRKLLYDVFKERFEQWFDSFWPGEEEIKEIMLKILDLLYNEDYEKIYEAEK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 polymer

description	PD3 Fab fragment heavy chain
formula_weight	27880.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MPMGSLQPLATLYLLGMLVASVLAEVQLVESGGGLVQPGGSLRLSCAASGFTFRNYWMNWVRQAPGKGLEWVANIKQDGSEKYYVDSVKGRFTISRDNAKNSFYLQMNSLRAEDTAVYYCARSSITARALFDCWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGGSGGSHHHHHHHH

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 polymer

description	PD3 Fab fragment light chain
formula_weight	25967.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MPMGSLQPLATLYLLGMLVASVLADIQLTQSPSFLSASVGDRVTITCRATQDISSYLAWYQQKPGKAPKLLIFTASTLQTGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYPWTFGQGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 5 polymer

description	Kappa light chain nanobody
formula_weight	17252.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MKKTAIAIAVALAGFATVAQAAPMGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSSHHHHHHHHEPEA

Source

organism	Lama glama
common_name	llama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

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	1

Entity 7 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	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	216

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	512440

fit	/app/data/saxs_computation/1z/11zw/11zw.fit
pddf	/app/data/pr_computation/1z/11zw/11zw.pr.out
profile	/app/data/saxs_computation/1z/11zw/11zw.dat

;Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody ;

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 polymer

Polymer

Source

Entity 6 branched

Entity 7 branched

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)