← Back to search

9qyi

Crystal structure of human S-adenosyl-L-homocysteine hydrolase complex with adenosine

Method: X-RAY DIFFRACTION D_max: 165.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qyi
deposition_date	2025-04-18
last_revision	2026-04-29
title	Crystal structure of human S-adenosyl-L-homocysteine hydrolase complex with adenosine
keywords	Protein dynamics, human SAHase, metal binding, AHCY, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	50.69 Å
rg_electron	50.80 Å
i0	2159210000.00
molecular_weight	388230.0 kDa
excluded_volume	485390 Å³
envelope_volume	600400 Å³
shell_volume	95603 Å³
envelope_diameter	173.0 Å
shell_rg	56.03 Å
envelope_rg	50.30 Å
shape_rg	50.83 Å
total_rg	50.84 Å
total_atoms	27195
n_residues	3440
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	165.2 Å
rg_real	50.71 Å
rg_real_error	1.50 Å
i0_real	2.1590e+09
i0_real_error	4.4230e+07
rg_reciprocal	50.65 Å
i0_reciprocal	2159000000.0000
total_estimate	0.8736
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.3 Å
skewness	0.307
kurtosis	-0.624
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	245200000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.676

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

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	30109

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	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2713

▶

6. Citations (1)

▶

length_a	81.761 Å
length_b	90.195 Å
length_c	124.550 Å
angle_alpha	96.23 °
angle_beta	89.57 °
angle_gamma	105.53 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.590 Å
resolution_low	123.780 Å
r_factor	0.1770
r_work	0.1768
r_free	0.2136

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