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9rit

Co-crystal of broadly neutralizing biparatopic VHH in complex with cardiotoxin (P01468) Naja pallida

Method: X-RAY DIFFRACTION D_max: 77.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rit
deposition_date	2025-06-11
title	Co-crystal of broadly neutralizing biparatopic VHH in complex with cardiotoxin (P01468) Naja pallida
keywords	nanobody, VHH, antibody, toxin, snake toxin, snake venom, neutralizing, cytotoxin, biparatopic; TOXIN
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	24.02 Å
rg_electron	23.19 Å
i0	28989700.00
molecular_weight	39870.0 kDa
excluded_volume	49378 Å³
envelope_volume	61845 Å³
shell_volume	22944 Å³
envelope_diameter	83.9 Å
shell_rg	29.44 Å
envelope_rg	23.17 Å
shape_rg	23.17 Å
total_rg	24.07 Å
total_atoms	2800
n_residues	356
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	77.8 Å
rg_real	23.94 Å
rg_real_error	0.54 Å
i0_real	2.8990e+07
i0_real_error	4.2640e+05
rg_reciprocal	23.96 Å
i0_reciprocal	28990000.0000
total_estimate	0.9017
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.195
kurtosis	-0.444
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	3490000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Variable Domain of Heavy-Chain only Antibody (VHH)
formula_weight	13832.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3094

QVQLQESGGGLVQAGGSLRLSCAASGRTFSSYAMAWFRQAPGKEREFVASISWNGDSTYYADSVKGRFTISGDNAKNTWYLQMKSLKPEDTAVYYCNTEDEGSGTYYEWGQGTQVTVSSENLYFQ

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 2 polymer

description	Cytotoxin 1
formula_weight	6838.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	270

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6. Citations (1)

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length_a	41.943 Å
length_b	54.905 Å
length_c	143.014 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 2 21
int_tables_number	17
crystal_system	orthorhombic

resolution	1.600 Å
resolution_low	51.260 Å
r_factor	0.2238
r_work	0.2220
r_free	0.2578

fit	/app/data/saxs_computation/ri/9rit/9rit.fit
pddf	/app/data/pr_computation/ri/9rit/9rit.pr.out
profile	/app/data/saxs_computation/ri/9rit/9rit.dat

Co-crystal of broadly neutralizing biparatopic VHH in complex with cardiotoxin (P01468) Naja pallida

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

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)