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9r1y

PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR GSK461364

Method: X-RAY DIFFRACTION D_max: 94.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r1y
deposition_date	2025-04-28
title	PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR GSK461364
keywords	SURFACE ENTROPY REDUCTION, SER, SMALL MOLECULE INHIBITOR, DRUG DESIGN, KINASE, SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE; TRANSFERASE
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	29.63 Å
rg_electron	29.00 Å
i0	149118000.00
molecular_weight	64573.0 kDa
excluded_volume	62370 Å³
envelope_volume	111520 Å³
shell_volume	32617 Å³
envelope_diameter	98.0 Å
shell_rg	35.61 Å
envelope_rg	29.04 Å
shape_rg	28.97 Å
total_rg	29.52 Å
total_atoms	4882
n_residues	585
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	94.2 Å
rg_real	29.67 Å
rg_real_error	0.69 Å
i0_real	1.4910e+08
i0_real_error	2.2480e+06
rg_reciprocal	29.65 Å
i0_reciprocal	149100000.0000
total_estimate	0.8936
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.2 Å
skewness	0.347
kurtosis	-0.539
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	32190000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.858

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Serine/threonine-protein kinase PLK1
formula_weight	36546.4 kDa
ec_number	2.7.11.21
mutation	K225D, K226A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	AAA,BBB
atom_count	5010

GSGKAGVPGVAAPGAPAAAPPAKEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKTLCGTPNYIAPEVLSDAGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPSSLDPSNRKPL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 non-polymer

description	5-[6-[(4-methylpiperazin-1-yl)methyl]benzimidazol-1-yl]-3-[(1~{R})-1-[2-(trifluoromethyl)phenyl]ethoxy]thiophene-2-carboxamide
formula_weight	543.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	56

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6. Citations (1)

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length_a	113.772 Å
length_b	104.174 Å
length_c	71.286 Å
angle_alpha	90.00 °
angle_beta	115.31 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.602 Å
resolution_low	42.428 Å
r_factor	—
r_work	0.1850
r_free	0.2178

fit	/app/data/saxs_computation/r1/9r1y/9r1y.fit
pddf	/app/data/pr_computation/r1/9r1y/9r1y.pr.out
profile	/app/data/saxs_computation/r1/9r1y/9r1y.dat