SAXSdb — 9u8g

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1. Structure Basics

entry_id	9u8g
deposition_date	2025-03-26
last_revision	2025-07-30
title	Crystal structure of TMPRSS2 in complex with nanobody77_10
keywords	Complex, Antibody, Host protease, ANTIVIRAL PROTEIN, 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	31.12 Å
rg_electron	30.24 Å
i0	196767000.00
molecular_weight	107900.0 kDa
excluded_volume	133330 Å³
envelope_volume	167260 Å³
shell_volume	44260 Å³
envelope_diameter	92.1 Å
shell_rg	39.01 Å
envelope_rg	29.83 Å
shape_rg	30.23 Å
total_rg	31.00 Å
total_atoms	7565
n_residues	984
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	91.1 Å
rg_real	30.86 Å
rg_real_error	0.40 Å
i0_real	1.9680e+08
i0_real_error	2.6560e+06
rg_reciprocal	30.97 Å
i0_reciprocal	196800000.0000
total_estimate	0.9110
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	44.7 Å
skewness	-0.022
kurtosis	-0.651
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	45990000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Transmembrane protease serine 2 non-catalytic chain
formula_weight	16054.7 kDa
mutation	S250D,S251D,R252D,Q253D, S254K
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	8240

MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Transmembrane protease serine 2 catalytic chain
formula_weight	27856.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFVEHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Nanobody
formula_weight	14793.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

AVQLQASGGGFVQPGGSLRLSCAASGKVVEQGLMGWFRQAPGKEREFVSAIQYDTKLEYYADSVKGRFTISRDNSKNTVYLQMNSLRAEDTATYYCATPQMWVQRDRDDRWYWGQGTQVTVSSGSHHHHHH

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Homo sapiens

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	nat
entity_count	2

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	599

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6. Citations (1)

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length_a	67.616 Å
length_b	69.827 Å
length_c	82.192 Å
angle_alpha	104.97 °
angle_beta	112.85 °
angle_gamma	102.10 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.000 Å
resolution_low	18.290 Å
r_factor	0.1949
r_work	0.1930
r_free	0.2298

fit	/app/data/saxs_computation/u8/9u8g/9u8g.fit
pddf	/app/data/pr_computation/u8/9u8g/9u8g.pr.out
profile	/app/data/saxs_computation/u8/9u8g/9u8g.dat

Crystal structure of TMPRSS2 in complex with nanobody77_10

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)