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9tp9

Crystal structure of integrin-linked kinase (ILK) in complex with Alpha-Parvin and dihydroPelitinib

Method: X-RAY DIFFRACTION D_max: 77.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tp9
deposition_date	2025-12-17
title	Crystal structure of integrin-linked kinase (ILK) in complex with Alpha-Parvin and dihydroPelitinib
keywords	pseudokinase, focal adhesion, ligand complex, kinase, drug target, CELL ADHESION; CELL ADHESION
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	23.75 Å
rg_electron	22.97 Å
i0	55894300.00
molecular_weight	41930.0 kDa
excluded_volume	42885 Å³
envelope_volume	67079 Å³
shell_volume	24725 Å³
envelope_diameter	82.7 Å
shell_rg	29.61 Å
envelope_rg	23.22 Å
shape_rg	22.57 Å
total_rg	24.31 Å
total_atoms	3620
n_residues	392
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	77.9 Å
rg_real	23.73 Å
rg_real_error	0.47 Å
i0_real	5.5890e+07
i0_real_error	7.0740e+05
rg_reciprocal	23.73 Å
i0_reciprocal	55890000.0000
total_estimate	0.8136
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	68.2 Å
skewness	0.327
kurtosis	-0.373
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	12660000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Scaffold protein ILK
formula_weight	30972.0 kDa
mutation	C422S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3937

MNKHSGIDFKQLNFLTKLNENHSGELWKGRWQGNDIVVKVLKVRDWSTRKSRDFNEECPRLRIFSHPNVLPVLGACQSPPAPHPTLITHWMPYGSLYNVLHEGTNFVVDQSQAVKFALDMARGMAFLHTLEPLIPRHALNSRSVMIDEDMTARISMADVKFSFQSPGRMYAPAWVAPEALQKKPEDTNRRSADMWSFAVLLWELVTREVPFADLSNMEIGMKVALEGLRPTIPPGISPHVSKLMKICMNEDPAKRPKFDMIVPILEKMQDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Alpha-parvin
formula_weight	14647.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SMDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYNLFTKYRNVE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	~{N}-[4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-3-cyano-7-ethoxy-quinolin-6-yl]-4-(dimethylamino)butanamide
formula_weight	469.9 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	292

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6. Citations (1)

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length_a	43.836 Å
length_b	118.522 Å
length_c	47.494 Å
angle_alpha	90.00 °
angle_beta	100.38 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.450 Å
resolution_low	40.520 Å
r_factor	0.1994
r_work	0.1984
r_free	0.2194

fit	/app/data/saxs_computation/tp/9tp9/9tp9.fit
pddf	/app/data/pr_computation/tp/9tp9/9tp9.pr.out
profile	/app/data/saxs_computation/tp/9tp9/9tp9.dat

Crystal structure of integrin-linked kinase (ILK) in complex with Alpha-Parvin and dihydroPelitinib

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 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)