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9qyj

Crystal structure of human S-adenosyl-L-homocysteine hydrolase in complex with adenosine and cadmium ions.

Method: X-RAY DIFFRACTION D_max: 168.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qyj
deposition_date	2025-04-18
last_revision	2026-04-29
title	Crystal structure of human S-adenosyl-L-homocysteine hydrolase in complex with adenosine and cadmium ions.
keywords	Protein dynamics, human SAHase, metal binding, AHCY, HYDROLASE; HYDROLASE
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	50.86 Å
rg_electron	50.93 Å
i0	2282700000.00
molecular_weight	392290.0 kDa
excluded_volume	486380 Å³
envelope_volume	600970 Å³
shell_volume	95690 Å³
envelope_diameter	172.6 Å
shell_rg	56.19 Å
envelope_rg	50.34 Å
shape_rg	50.93 Å
total_rg	51.06 Å
total_atoms	27165
n_residues	3436
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	168.0 Å
rg_real	50.88 Å
rg_real_error	1.93 Å
i0_real	2.2830e+09
i0_real_error	5.0580e+07
rg_reciprocal	50.83 Å
i0_reciprocal	2283000000.0000
total_estimate	0.8792
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.2 Å
skewness	0.305
kurtosis	-0.624
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	268600000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.806

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Adenosylhomocysteinase
formula_weight	47640.8 kDa
ec_number	3.13.2.1
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,D,E,F,G,C,H
atom_count	28621

SDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQNHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSCDGPFKPDHYRY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	ADENOSINE
formula_weight	267.2 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	CADMIUM ION
formula_weight	112.4 kDa
src_method	syn
entity_count	45

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	8

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1383

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6. Citations (1)

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length_a	82.186 Å
length_b	89.710 Å
length_c	124.297 Å
angle_alpha	96.44 °
angle_beta	89.92 °
angle_gamma	105.82 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.930 Å
resolution_low	74.590 Å
r_factor	0.1765
r_work	0.1758
r_free	0.2441

fit	/app/data/saxs_computation/qy/9qyj/9qyj.fit
pddf	/app/data/pr_computation/qy/9qyj/9qyj.pr.out
profile	/app/data/saxs_computation/qy/9qyj/9qyj.dat