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9r1x

PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR BI 2536

Method: X-RAY DIFFRACTION D_max: 93.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r1x
deposition_date	2025-04-28
title	PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR BI 2536
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	29.72 Å
rg_electron	28.88 Å
i0	74341200.00
molecular_weight	68833.0 kDa
excluded_volume	86764 Å³
envelope_volume	109720 Å³
shell_volume	32327 Å³
envelope_diameter	98.3 Å
shell_rg	35.42 Å
envelope_rg	28.90 Å
shape_rg	28.88 Å
total_rg	29.53 Å
total_atoms	4840
n_residues	584
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	93.6 Å
rg_real	29.76 Å
rg_real_error	0.64 Å
i0_real	7.4340e+07
i0_real_error	1.1140e+06
rg_reciprocal	29.75 Å
i0_reciprocal	74340000.0000
total_estimate	0.8954
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.0 Å
skewness	0.345
kurtosis	-0.525
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	22860000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.838

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4975

GSGKAGVPGVAAPGAPAAAPPAKEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKTLCGTPNYIAPEVLSDAGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPSSLDPSNRKPL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 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 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	7

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	64

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6. Citations (1)

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length_a	112.515 Å
length_b	104.497 Å
length_c	71.329 Å
angle_alpha	90.00 °
angle_beta	115.63 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.840 Å
resolution_low	42.100 Å
r_factor	0.2217
r_work	0.2188
r_free	0.2775

fit	/app/data/saxs_computation/r1/9r1x/9r1x.fit
pddf	/app/data/pr_computation/r1/9r1x/9r1x.pr.out
profile	/app/data/saxs_computation/r1/9r1x/9r1x.dat