← Back to search

9r8b

CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN

Method: X-RAY DIFFRACTION D_max: 96.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9r8b
deposition_date	2025-05-16
title	CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN
keywords	;DESIGN ANKYRIN REPEAT PROTEIN, DARPIN, SMALL MOLECULE INHIBITOR, DRUG DESIGN, KINASE, SERINE/THREONINE-PROTEIN KINASE, KINASE DOMAIN, TRANSFERASE ;; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.81 Å
rg_electron	30.07 Å
i0	275345000.00
molecular_weight	88739.0 kDa
excluded_volume	85915 Å³
envelope_volume	152730 Å³
shell_volume	41178 Å³
envelope_diameter	101.0 Å
shell_rg	38.13 Å
envelope_rg	30.26 Å
shape_rg	30.07 Å
total_rg	30.59 Å
total_atoms	6735
n_residues	843
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	96.3 Å
rg_real	30.65 Å
rg_real_error	0.59 Å
i0_real	2.7530e+08
i0_real_error	3.9520e+06
rg_reciprocal	30.72 Å
i0_reciprocal	275400000.0000
total_estimate	0.9033
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	41.5 Å
skewness	0.146
kurtosis	-0.489
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	39530000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.952

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Serine/threonine-protein kinase PLK1
formula_weight	35972.9 kDa
ec_number	2.7.11.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7196

GSAAPPAKEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKTLCGTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPSSLDPSNRKPLTVLNK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN), variant 3H10
formula_weight	17836.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILIANGADVNAVDNTGLTPLHLAAVSGHLEIVEVLLKHGADVDAADVYGFTPLHLAAMTGHLEIVEVLLKYGADVNAFDMTGSTPLHLAADEGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAKSCRN

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	;(2~{Z})-2-cyano-2-[3-ethyl-5-[(~{E})-[2-[methyl-(1-methylpiperidin-4-yl)amino]pyridin-4-yl]iminomethyl]-4-oxidanylidene-1,3-thiazol-2-ylidene]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide ;
formula_weight	523.6 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	388

▶

6. Citations (2)

▶

length_a	61.072 Å
length_b	136.899 Å
length_c	140.729 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.200 Å
resolution_low	68.540 Å
r_factor	0.1907
r_work	0.1882
r_free	0.2385

fit	/app/data/saxs_computation/r8/9r8b/9r8b.fit
pddf	/app/data/pr_computation/r8/9r8b/9r8b.pr.out
profile	/app/data/saxs_computation/r8/9r8b/9r8b.dat

CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN

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 (2)

7. Files & Curves (10)

Files (7)

Curves (3)