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9pzi

Crystal Structure of synthetic antibody COP-2 in complex with the C-terminal domain of Clostridium perfringens enterotoxin

Method: X-RAY DIFFRACTION D_max: 139.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pzi
deposition_date	2025-08-11
title	Crystal Structure of synthetic antibody COP-2 in complex with the C-terminal domain of Clostridium perfringens enterotoxin
keywords	ENTEROTOXIN, SYNTHETIC ANTIBODY, TOXIN, IMMUNE SYSTEM-TOXIN complex; IMMUNE SYSTEM/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	42.82 Å
rg_electron	42.52 Å
i0	493075000.00
molecular_weight	181390.0 kDa
excluded_volume	226540 Å³
envelope_volume	328510 Å³
shell_volume	64465 Å³
envelope_diameter	145.3 Å
shell_rg	47.87 Å
envelope_rg	41.43 Å
shape_rg	42.53 Å
total_rg	42.75 Å
total_atoms	25197
n_residues	1671
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	139.2 Å
rg_real	42.71 Å
rg_real_error	1.09 Å
i0_real	4.9310e+08
i0_real_error	9.0960e+06
rg_reciprocal	42.82 Å
i0_reciprocal	493100000.0000
total_estimate	0.8996
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.7 Å
skewness	0.196
kurtosis	-0.517
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	37540000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.938

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	COP-2 Light chain
formula_weight	26053.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,A,E
atom_count	25529

MKKNIAFLLASMFVFSIATNAYASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYEWAPVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	COP-2 Heavy chain
formula_weight	27799.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,B,F

MKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVASISSYSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYWSWYNSSHYIYSALDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Heat-labile enterotoxin B chain
formula_weight	15114.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,I,H

MSTDIEKEILDLAAATERLNLTDALNSNPAGNLYDWRSSNSYPWTQKLNLHLTITATGQKYRILASKIVDFNIYSNNFNNLVKLEQSLGDGVKDHYVDISLDAGQYVLVMKANSSYSGNYPYSILFQKFGLVPR

Source

organism	Clostridium perfringens
ncbi_taxonomy_id	1502
host_organism	Trichoplusia ni

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	323

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6. Citations (1)

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length_a	111.475 Å
length_b	198.520 Å
length_c	115.800 Å
angle_alpha	90.00 °
angle_beta	109.72 °
angle_gamma	90.00 °
z_pdb	12

space_group	I 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.500 Å
resolution_low	29.740 Å
r_factor	—
r_work	0.1783
r_free	0.2248

fit	/app/data/saxs_computation/pz/9pzi/9pzi.fit
pddf	/app/data/pr_computation/pz/9pzi/9pzi.pr.out
profile	/app/data/saxs_computation/pz/9pzi/9pzi.dat

Crystal Structure of synthetic antibody COP-2 in complex with the C-terminal domain of Clostridium perfringens enterotoxin

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

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)