SAXSdb — 9qcv

▼

1. Structure Basics

entry_id	9qcv
deposition_date	2025-03-05
title	Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP
keywords	Complex, cell cycle, kinase, TRANSFERASE; TRANSFERASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.31 Å
rg_electron	34.83 Å
i0	274358000.00
molecular_weight	137930.0 kDa
excluded_volume	174510 Å³
envelope_volume	219930 Å³
shell_volume	52486 Å³
envelope_diameter	123.2 Å
shell_rg	41.32 Å
envelope_rg	34.61 Å
shape_rg	34.80 Å
total_rg	35.36 Å
total_atoms	9710
n_residues	1197
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	118.3 Å
rg_real	35.32 Å
rg_real_error	0.81 Å
i0_real	2.7440e+08
i0_real_error	4.9330e+06
rg_reciprocal	35.32 Å
i0_reciprocal	274400000.0000
total_estimate	0.6807
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	42.1 Å
skewness	0.405
kurtosis	-0.132
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0002
highest_alpha	92770000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.999; Smooth: 0.824

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (8)

Entity 1 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	K
atom_count	9759

SNAMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Cyclin-A2
formula_weight	48867.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SNAMLGNSAPGPATREAGSALLALQQTALQEDQENINPEKAAPVQQPRTRAALAVLKSGNPRGLAQQQRPKTRRVAPLKDLPVNDEHVTVPPWKANSKQPAFTIHVDEAEKEAQKKPAESQKIEREDALAFNSAISLPGPRKPLVPLDYPMDGSFESPHTMDMSIVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	CDK-activating kinase assembly factor MAT1
formula_weight	38132.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MGSSHHHHHHENLYFQSNAMDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFEDPTVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEEVEEIVFNLTNNVDLDNTKKKMEIYQKENKDVIQKNKLKLTREQEELEEALEVERQENEQRRLFIQKEEQLQQILKRKNKQAFLDELESSDLPVALLLAQHKDRSTQLEMQLEKPKPVKPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDAFSGLFWQPS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 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 5 polymer

description	Cyclin-dependent kinase 7
formula_weight	43651.1 kDa
ec_number	2.7.11.22,2.7.11.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 6 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	49

▶

6. Citations (1)

▶

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

resolution	2.50 Å
resolution_method	—
num_particles	282506

fit	/app/data/saxs_computation/qc/9qcv/9qcv.fit
pddf	/app/data/pr_computation/qc/9qcv/9qcv.pr.out
profile	/app/data/saxs_computation/qc/9qcv/9qcv.dat

Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)