SAXSdb — 9qjn

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1. Structure Basics

entry_id	9qjn
deposition_date	2025-03-19
title	Cryo-EM structure of the human CAK bound to OTS964
keywords	kinase, cyclin-dependent kinase, inhibitor, CELL CYCLE; CELL CYCLE
method	ELECTRON MICROSCOPY

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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	27.90 Å
rg_electron	26.95 Å
i0	80509300.00
molecular_weight	72485.0 kDa
excluded_volume	91716 Å³
envelope_volume	110650 Å³
shell_volume	33940 Å³
envelope_diameter	94.5 Å
shell_rg	34.51 Å
envelope_rg	27.01 Å
shape_rg	26.93 Å
total_rg	27.81 Å
total_atoms	5104
n_residues	630
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	89.2 Å
rg_real	27.81 Å
rg_real_error	0.54 Å
i0_real	8.0510e+07
i0_real_error	1.0020e+06
rg_reciprocal	27.84 Å
i0_reciprocal	80510000.0000
total_estimate	0.7087
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	32.9 Å
skewness	0.269
kurtosis	-0.418
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	25890000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 1.000; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	CDK-activating kinase assembly factor MAT1
formula_weight	10234.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	5246

SNAPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDAFSGLFWQPS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Cyclin-H
formula_weight	37721.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKSKHEEEEWTDDDLVESL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Cyclin-dependent kinase 7
formula_weight	39362.6 kDa
ec_number	2.7.11.22,2.7.11.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

SNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 non-polymer

description	OTS964
formula_weight	392.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	142

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6. Citations (1)

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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	2.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	340642

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

Cryo-EM structure of the human CAK 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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)