SAXSdb — 9t3r

▼

1. Structure Basics

entry_id	9t3r
deposition_date	2025-10-29
title	Structure of human HER2 in complex with EPS232 Fab
keywords	Antibody Fab, Complex, cancer, extracellular domain., ANTITUMOR PROTEIN; ANTITUMOR PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.72 Å
rg_electron	31.39 Å
i0	88334000.00
molecular_weight	72378.0 kDa
excluded_volume	89680 Å³
envelope_volume	115490 Å³
shell_volume	31789 Å³
envelope_diameter	106.3 Å
shell_rg	37.14 Å
envelope_rg	30.95 Å
shape_rg	31.41 Å
total_rg	31.83 Å
total_atoms	5077
n_residues	663
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

▼

3. P(r) Analysis (GNOM)

dmax	103.8 Å
rg_real	31.80 Å
rg_real_error	0.84 Å
i0_real	8.8330e+07
i0_real_error	1.3800e+06
rg_reciprocal	31.77 Å
i0_reciprocal	88330000.0000
total_estimate	0.8922
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.1 Å
skewness	0.321
kurtosis	-0.603
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	15450000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.939

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ig-like domain-containing protein
formula_weight	22677.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	5077

QSVLTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYTVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSSLVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	EPS232 Fab HC
formula_weight	28701.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWIGWINAGNGNTKYSQKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYCARDFSSQVATAAVDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTSGQAGQHHHHHHGAEQKLISEEDLGGLNDIFEAQKIEWHE

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Receptor tyrosine-protein kinase erbB-2
formula_weight	70249.7 kDa
ec_number	2.7.10.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

▶

6. Citations (1)

▶

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	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	179482

fit	/app/data/saxs_computation/t3/9t3r/9t3r.fit
pddf	/app/data/pr_computation/t3/9t3r/9t3r.pr.out
profile	/app/data/saxs_computation/t3/9t3r/9t3r.dat

Structure of human HER2 in complex with EPS232 Fab

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)