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9z2d

Mitochondrial Creatine Kinase in complex with ADP, creatine, and uncompetitive inhibitor uci

Method: ELECTRON MICROSCOPY D_max: 149.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z2d
deposition_date	2025-11-04
title	Mitochondrial Creatine Kinase in complex with ADP, creatine, and uncompetitive inhibitor uci
keywords	Kinase, inhibitor, TRANSFERASE-INHIBITOR complex, transition state analog; TRANSFERASE/INHIBITOR
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	48.04 Å
rg_electron	47.37 Å
i0	1654400000.00
molecular_weight	322760.0 kDa
excluded_volume	395960 Å³
envelope_volume	530400 Å³
shell_volume	89036 Å³
envelope_diameter	162.0 Å
shell_rg	55.63 Å
envelope_rg	46.50 Å
shape_rg	47.21 Å
total_rg	48.16 Å
total_atoms	43968
n_residues	2944
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	149.6 Å
rg_real	47.70 Å
rg_real_error	0.82 Å
i0_real	1.6540e+09
i0_real_error	2.5490e+07
rg_reciprocal	48.04 Å
i0_reciprocal	1655000000.0000
total_estimate	0.8915
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.5 Å
skewness	0.062
kurtosis	-0.507
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	161600000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.899

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Creatine kinase U-type, mitochondrial
formula_weight	47598.7 kDa
ec_number	2.7.3.2
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	44384

MGSSHHHHHHSSGLVPRGSHMENLYFQGAASERRRLYPPSAEYPDLRKHNNCMASHLTPAVYARLCDKTTPTGWTLDQCIQTGVDNPGHPFIKTVGMVAGDEETYEVFADLFDPVIQERHNGYDPRTMKHTTDLDASKIRSGYFDERYVLSSRVRTGRSIRGLSLPPACTRAERREVERVVVDALSGLKGDLAGRYYRLSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNEKSFLIWVNEEDHTRVISMEKGGNMKRVFERFCRGLKEVERLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHIKLPLLSKDSRFPKILENLRLQKRGTGGVDTAATGGVFDISNLDRLGKSEVELVQLVIDGVNYLIDCERRLERGQDIRIPTPVIHTKHGSSDYKDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE
formula_weight	131.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	[4-(2-amino-6-methylpyrimidin-4-yl)piperazin-1-yl](3,5,7-trimethyl-1H-indol-2-yl)methanone
formula_weight	378.5 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

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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	2.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.60 Å
resolution_method	—
num_particles	1083440

fit	/app/data/saxs_computation/z2/9z2d/9z2d.fit
pddf	/app/data/pr_computation/z2/9z2d/9z2d.pr.out
profile	/app/data/saxs_computation/z2/9z2d/9z2d.dat