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9tpd

Crystal structure of integrin-linked kinase (ILK) in complex with alpha-parvin and a cyano-quinoline ligand

Method: X-RAY DIFFRACTION D_max: 81.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tpd
deposition_date	2025-12-17
title	Crystal structure of integrin-linked kinase (ILK) in complex with alpha-parvin and a cyano-quinoline ligand
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	24.05 Å
rg_electron	23.18 Å
i0	32565400.00
molecular_weight	45338.0 kDa
excluded_volume	57279 Å³
envelope_volume	68272 Å³
shell_volume	24908 Å³
envelope_diameter	84.3 Å
shell_rg	29.67 Å
envelope_rg	23.27 Å
shape_rg	23.19 Å
total_rg	23.94 Å
total_atoms	6344
n_residues	395
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	81.5 Å
rg_real	24.02 Å
rg_real_error	0.52 Å
i0_real	3.2570e+07
i0_real_error	4.6770e+05
rg_reciprocal	24.03 Å
i0_reciprocal	32570000.0000
total_estimate	0.8804
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.8 Å
skewness	0.336
kurtosis	-0.335
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	10050000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	6644

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	4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-6-piperazin-1-yl-quinoline-3-carbonitrile
formula_weight	381.8 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

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

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	261

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6. Citations (1)

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length_a	43.860 Å
length_b	118.370 Å
length_c	47.600 Å
angle_alpha	90.00 °
angle_beta	100.91 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.500 Å
resolution_low	43.070 Å
r_factor	0.1915
r_work	0.1890
r_free	0.2150

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

Crystal structure of integrin-linked kinase (ILK) in complex with alpha-parvin and a cyano-quinoline ligand

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 non-polymer

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)