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9plk

Interaction of human CYP3A4 with the drug darifenacin

Method: X-RAY DIFFRACTION D_max: 71.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9plk
deposition_date	2025-07-15
title	Interaction of human CYP3A4 with the drug darifenacin
keywords	cytochrome P450, CYP3A4, substrate, drug, darifenacin, 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	23.25 Å
rg_electron	22.24 Å
i0	82186300.00
molecular_weight	48974.0 kDa
excluded_volume	48155 Å³
envelope_volume	77426 Å³
shell_volume	28108 Å³
envelope_diameter	74.9 Å
shell_rg	29.92 Å
envelope_rg	22.44 Å
shape_rg	22.24 Å
total_rg	22.92 Å
total_atoms	3715
n_residues	453
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	71.4 Å
rg_real	23.11 Å
rg_real_error	0.30 Å
i0_real	8.2190e+07
i0_real_error	1.1500e+06
rg_reciprocal	23.14 Å
i0_reciprocal	82190000.0000
total_estimate	0.9050
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.137
kurtosis	-0.527
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	13260000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Cytochrome P450 3A4
formula_weight	55757.8 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
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3749

MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

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	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	darifenacin
formula_weight	426.6 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

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6. Citations (1)

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length_a	75.770 Å
length_b	101.122 Å
length_c	123.880 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	2.250 Å
resolution_low	39.820 Å
r_factor	0.2298
r_work	0.2277
r_free	0.2716

fit	/app/data/saxs_computation/pl/9plk/9plk.fit
pddf	/app/data/pr_computation/pl/9plk/9plk.pr.out
profile	/app/data/saxs_computation/pl/9plk/9plk.dat