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13lv

Structure of PKMYT1 bound to allosteric inhibitor P29-(S)

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13lv
deposition_date	2026-05-13
last_revision	2026-06-10
title	Structure of PKMYT1 bound to allosteric inhibitor P29-(S)
keywords	kinase, PKMYT1, inhibitor, allosteric, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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	21.05 Å
rg_electron	20.33 Å
i0	33595100.00
molecular_weight	29638.0 kDa
excluded_volume	28572 Å³
envelope_volume	48371 Å³
shell_volume	20336 Å³
envelope_diameter	74.1 Å
shell_rg	26.47 Å
envelope_rg	20.60 Å
shape_rg	20.27 Å
total_rg	21.06 Å
total_atoms	2262
n_residues	286
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	73.2 Å
rg_real	21.08 Å
rg_real_error	0.45 Å
i0_real	3.3600e+07
i0_real_error	4.6250e+05
rg_reciprocal	21.07 Å
i0_reciprocal	33590000.0000
total_estimate	0.8558
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.453
kurtosis	-0.169
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	10480000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
formula_weight	32237.7 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2282

GPGSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(4S)-1-cyclopentyl-4-(4-hydroxyphenyl)-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one
formula_weight	297.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3

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6. Citations (1)

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length_a	60.398 Å
length_b	60.398 Å
length_c	379.379 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.220 Å
resolution_low	37.640 Å
r_factor	0.2292
r_work	0.2274
r_free	0.2691

fit	/app/data/saxs_computation/3l/13lv/13lv.fit
pddf	/app/data/pr_computation/3l/13lv/13lv.pr.out
profile	/app/data/saxs_computation/3l/13lv/13lv.dat

Structure of PKMYT1 bound to allosteric inhibitor P29-(S)

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