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9z28

KHK Bound to Compound 7

Method: X-RAY DIFFRACTION D_max: 100.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z28
deposition_date	2025-11-04
title	KHK Bound to Compound 7
keywords	Inhibitor, Fructose, Metabolism, Phosphorylation, 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	29.36 Å
rg_electron	29.22 Å
i0	141001000.00
molecular_weight	61298.0 kDa
excluded_volume	58346 Å³
envelope_volume	100950 Å³
shell_volume	30296 Å³
envelope_diameter	100.8 Å
shell_rg	34.95 Å
envelope_rg	29.16 Å
shape_rg	29.27 Å
total_rg	29.54 Å
total_atoms	4620
n_residues	599
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	100.5 Å
rg_real	29.56 Å
rg_real_error	1.02 Å
i0_real	1.4100e+08
i0_real_error	2.4040e+06
rg_reciprocal	29.48 Å
i0_reciprocal	141000000.0000
total_estimate	0.7518
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.9 Å
skewness	0.501
kurtosis	-0.470
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	27270000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ketohexokinase
formula_weight	34076.6 kDa
ec_number	2.7.1.3
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4831

MGSSHHHHHHSSGLVPRGSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	4-methyl-2-[(2S)-2-methylazetidin-1-yl]-6,7-dihydro-5H-cyclopenta[d]pyrimidine
formula_weight	203.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	7

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	208

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6. Citations (1)

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length_a	83.003 Å
length_b	86.500 Å
length_c	137.423 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.150 Å
resolution_low	45.150 Å
r_factor	0.2008
r_work	0.1995
r_free	0.2249

fit	/app/data/saxs_computation/z2/9z28/9z28.fit
pddf	/app/data/pr_computation/z2/9z28/9z28.pr.out
profile	/app/data/saxs_computation/z2/9z28/9z28.dat

KHK Bound to Compound 7

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