← Back to search

9qjj

Cryo-EM structure of CDK2-cyclin A bound to OTS964

Method: ELECTRON MICROSCOPY D_max: 81.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qjj
deposition_date	2025-03-19
title	Cryo-EM structure of CDK2-cyclin A bound to OTS964
keywords	kinase, cyclin-dependent kinase, inhibitor, CELL CYCLE; CELL CYCLE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.58 Å
rg_electron	25.52 Å
i0	58043100.00
molecular_weight	62717.0 kDa
excluded_volume	80075 Å³
envelope_volume	95052 Å³
shell_volume	30806 Å³
envelope_diameter	87.0 Å
shell_rg	33.19 Å
envelope_rg	25.55 Å
shape_rg	25.51 Å
total_rg	26.48 Å
total_atoms	4426
n_residues	546
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	81.2 Å
rg_real	26.49 Å
rg_real_error	0.44 Å
i0_real	5.8040e+07
i0_real_error	7.0600e+05
rg_reciprocal	26.52 Å
i0_reciprocal	58040000.0000
total_estimate	0.9127
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.220
kurtosis	-0.565
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	18930000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.970

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cyclin-A2
formula_weight	48867.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4481

SNAMLGNSAPGPATREAGSALLALQQTALQEDQENINPEKAAPVQQPRTRAALAVLKSGNPRGLAQQQRPKTRRVAPLKDLPVNDEHVTVPPWKANSKQPAFTIHVDEAEKEAQKKPAESQKIEREDALAFNSAISLPGPRKPLVPLDYPMDGSFESPHTMDMSIVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Cyclin-dependent kinase 2
formula_weight	34248.8 kDa
ec_number	2.7.11.22
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SNAMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	OTS964
formula_weight	392.5 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	55

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.50 Å
resolution_method	—
num_particles	503775

fit	/app/data/saxs_computation/qj/9qjj/9qjj.fit
pddf	/app/data/pr_computation/qj/9qjj/9qjj.pr.out
profile	/app/data/saxs_computation/qj/9qjj/9qjj.dat

Cryo-EM structure of CDK2-cyclin A bound to OTS964

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)