SAXSdb — 9z0f

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1. Structure Basics

entry_id	9z0f
deposition_date	2025-10-31
title	Crystal structure of Trastuzumab Fc conjugated to Linker-Payload
keywords	Trastuzumab, ADC, Fc, IgG1, antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
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	25.89 Å
rg_electron	24.93 Å
i0	78244400.00
molecular_weight	46449.0 kDa
excluded_volume	45030 Å³
envelope_volume	80223 Å³
shell_volume	26756 Å³
envelope_diameter	77.7 Å
shell_rg	32.20 Å
envelope_rg	24.49 Å
shape_rg	24.92 Å
total_rg	25.57 Å
total_atoms	3511
n_residues	414
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	77.0 Å
rg_real	25.75 Å
rg_real_error	0.48 Å
i0_real	7.8240e+07
i0_real_error	9.1140e+05
rg_reciprocal	25.79 Å
i0_reciprocal	78250000.0000
total_estimate	0.9180
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.4 Å
skewness	0.057
kurtosis	-0.674
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	7943000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Trastuzumab Fc
formula_weight	23822.0 kDa
mutation	S375C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3543

LLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNCVSLTCLVKGFYPCDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 polymer

description	Trastuzumab Fc
formula_weight	23979.2 kDa
mutation	S375C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

LLGGPSVFLFPPKPKDTLMIRRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNCVSLTCLVKGFYPCDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 branched

description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1463.3 kDa
src_method	man
entity_count	1

Entity 4 branched

description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1463.3 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	;N-({[4-({N-[3-(2,5-dioxopyrrolidin-1-yl)propanoyl]-L-alanyl-L-alanyl}amino)phenyl]methoxy}carbonyl)-N-methyl-L-valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide ;
formula_weight	1162.4 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (1)

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length_a	49.458 Å
length_b	79.590 Å
length_c	138.112 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.460 Å
resolution_low	68.960 Å
r_factor	0.2500
r_work	0.2488
r_free	0.2720

fit	/app/data/saxs_computation/z0/9z0f/9z0f.fit
pddf	/app/data/pr_computation/z0/9z0f/9z0f.pr.out
profile	/app/data/saxs_computation/z0/9z0f/9z0f.dat

Crystal structure of Trastuzumab Fc conjugated to Linker-Payload

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)