SAXSdb — 9z2a

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1. Structure Basics

entry_id	9z2a
deposition_date	2025-11-04
title	KHK Bound to Compound 12
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	29.25 Å
rg_electron	29.11 Å
i0	138599000.00
molecular_weight	61164.0 kDa
excluded_volume	58426 Å³
envelope_volume	99933 Å³
shell_volume	30083 Å³
envelope_diameter	101.6 Å
shell_rg	34.91 Å
envelope_rg	29.06 Å
shape_rg	29.16 Å
total_rg	29.42 Å
total_atoms	4618
n_residues	600
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	100.3 Å
rg_real	29.45 Å
rg_real_error	1.00 Å
i0_real	1.3860e+08
i0_real_error	2.4150e+06
rg_reciprocal	29.37 Å
i0_reciprocal	138600000.0000
total_estimate	0.7501
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.9 Å
skewness	0.505
kurtosis	-0.459
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	27300000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.645; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 0.839; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	4997

MGSSHHHHHHSSGLVPRGSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(3M)-3-{2-[(2S)-2-methylazetidin-1-yl]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl}benzene-1-sulfonamide
formula_weight	344.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	beta-D-fructofuranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	354

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6. Citations (1)

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length_a	82.566 Å
length_b	85.745 Å
length_c	136.313 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	2.000 Å
resolution_low	23.500 Å
r_factor	0.2156
r_work	0.2149
r_free	0.2369

fit	/app/data/saxs_computation/z2/9z2a/9z2a.fit
pddf	/app/data/pr_computation/z2/9z2a/9z2a.pr.out
profile	/app/data/saxs_computation/z2/9z2a/9z2a.dat

KHK Bound to Compound 12

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