← Back to search

9r8c

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: 98.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9r8c
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, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.71 Å
rg_electron	29.90 Å
i0	136970000.00
molecular_weight	95354.0 kDa
excluded_volume	120590 Å³
envelope_volume	149630 Å³
shell_volume	40719 Å³
envelope_diameter	99.1 Å
shell_rg	37.93 Å
envelope_rg	29.98 Å
shape_rg	29.87 Å
total_rg	30.74 Å
total_atoms	6720
n_residues	839
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	98.2 Å
rg_real	30.54 Å
rg_real_error	0.61 Å
i0_real	1.3700e+08
i0_real_error	1.9630e+06
rg_reciprocal	30.61 Å
i0_reciprocal	137000000.0000
total_estimate	0.8991
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.5 Å
skewness	0.135
kurtosis	-0.493
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	40210000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.985

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

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	7107

GSAAPPAKEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKTLCGTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPSSLDPSNRKPLTVLNK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda ascovirus 1a

Entity 2 polymer

description	DESIGNED ANKYRIN REPEAT PROTEIN 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	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
formula_weight	521.7 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	329

▶

6. Citations (2)

▶

length_a	62.605 Å
length_b	135.302 Å
length_c	136.700 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	2.243 Å
resolution_low	48.128 Å
r_factor	—
r_work	0.1882
r_free	0.2360

fit	/app/data/saxs_computation/r8/9r8c/9r8c.fit
pddf	/app/data/pr_computation/r8/9r8c/9r8c.pr.out
profile	/app/data/saxs_computation/r8/9r8c/9r8c.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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)