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9v90

Crystal structure of the PDZ tandem of syntenin in complex with PDZ2 inhibitor

Method: X-RAY DIFFRACTION D_max: 92.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v90
deposition_date	2025-05-30
title	Crystal structure of the PDZ tandem of syntenin in complex with PDZ2 inhibitor
keywords	Syntenin-1, PDZ domain, SIGNALING PROTEIN; SIGNALING PROTEIN
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	25.47 Å
rg_electron	24.84 Å
i0	22460000.00
molecular_weight	36181.0 kDa
excluded_volume	45403 Å³
envelope_volume	57486 Å³
shell_volume	20490 Å³
envelope_diameter	92.6 Å
shell_rg	30.12 Å
envelope_rg	24.57 Å
shape_rg	24.85 Å
total_rg	25.45 Å
total_atoms	2538
n_residues	326
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	92.7 Å
rg_real	25.55 Å
rg_real_error	0.90 Å
i0_real	2.2460e+07
i0_real_error	3.6000e+05
rg_reciprocal	25.53 Å
i0_reciprocal	22460000.0000
total_estimate	0.7542
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	22.4 Å
skewness	0.384
kurtosis	-0.300
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	9711000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.685; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.746; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Syntenin-1
formula_weight	17717.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3087

GIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2~{S})-2-[[(2~{S})-3-methyl-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)butanoyl]amino]propanoic acid
formula_weight	304.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	331

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6. Citations (1)

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length_a	59.869 Å
length_b	30.088 Å
length_c	91.056 Å
angle_alpha	90.00 °
angle_beta	90.85 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.400 Å
resolution_low	29.930 Å
r_factor	0.1864
r_work	0.1847
r_free	0.2202

fit	/app/data/saxs_computation/v9/9v90/9v90.fit
pddf	/app/data/pr_computation/v9/9v90/9v90.pr.out
profile	/app/data/saxs_computation/v9/9v90/9v90.dat

Crystal structure of the PDZ tandem of syntenin in complex with PDZ2 inhibitor

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