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9yk4

Crystal structure of CYP3A4 bound to imidazole and tetraethylene glycol

Method: X-RAY DIFFRACTION D_max: 83.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yk4
deposition_date	2025-10-06
title	Crystal structure of CYP3A4 bound to imidazole and tetraethylene glycol
keywords	cytochrome P450, CYP3A4, imidazole, tetraethyelene glycol, complex, OXIDOREDUCTASE; OXIDOREDUCTASE
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	23.83 Å
rg_electron	22.61 Å
i0	45635300.00
molecular_weight	55596.0 kDa
excluded_volume	71005 Å³
envelope_volume	81465 Å³
shell_volume	29028 Å³
envelope_diameter	76.0 Å
shell_rg	30.47 Å
envelope_rg	22.89 Å
shape_rg	22.60 Å
total_rg	23.58 Å
total_atoms	3904
n_residues	466
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	83.7 Å
rg_real	24.54 Å
rg_real_error	0.26 Å
i0_real	4.5430e+07
i0_real_error	4.9300e+05
rg_reciprocal	23.72 Å
i0_reciprocal	45640000.0000
total_estimate	0.6661
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.8 Å
skewness	0.411
kurtosis	0.100
angular_range	— – 0.3350 Å⁻¹
current_alpha	4.5000
highest_alpha	10800000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 0.908; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.677

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Cytochrome P450 3A4
formula_weight	55741.8 kDa
ec_number	1.14.14.1,1.14.14.56,1.14.14.73,1.14.14.55
mutation	residues 3-22 deleted, C-terminal 4-histidine tag, C468S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4184

MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPSKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	nat
entity_count	1

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	14

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	214

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6. Citations (1)

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length_a	77.109 Å
length_b	99.000 Å
length_c	133.440 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	1.780 Å
resolution_low	40.570 Å
r_factor	0.1854
r_work	0.1837
r_free	0.2182

fit	/app/data/saxs_computation/yk/9yk4/9yk4.fit
pddf	/app/data/pr_computation/yk/9yk4/9yk4.pr.out
profile	/app/data/saxs_computation/yk/9yk4/9yk4.dat