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9sck

Structure of Carnitine-O-acetyltransferase in complex with 6-benzyl-2-(naphthalen-1-yl)thieno[2,3-c]pyridin-6-ium

Method: X-RAY DIFFRACTION D_max: 82.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sck
deposition_date	2025-08-11
title	Structure of Carnitine-O-acetyltransferase in complex with 6-benzyl-2-(naphthalen-1-yl)thieno[2,3-c]pyridin-6-ium
keywords	CrAT, complex, inhibitor, reversible, transferase; TRANSFERASE
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	25.94 Å
rg_electron	24.83 Å
i0	72764800.00
molecular_weight	67746.0 kDa
excluded_volume	85244 Å³
envelope_volume	99689 Å³
shell_volume	32656 Å³
envelope_diameter	84.9 Å
shell_rg	32.98 Å
envelope_rg	25.11 Å
shape_rg	24.87 Å
total_rg	25.59 Å
total_atoms	9487
n_residues	591
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	82.5 Å
rg_real	25.85 Å
rg_real_error	0.50 Å
i0_real	7.2760e+07
i0_real_error	1.1340e+06
rg_reciprocal	25.88 Å
i0_reciprocal	72770000.0000
total_estimate	0.8983
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.252
kurtosis	-0.393
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	21800000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Carnitine O-acetyltransferase
formula_weight	69902.9 kDa
ec_number	2.3.1.137,2.3.1.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10367

MRGSHHHHHHTDPLPRLPVPPLQQSLDHYLKALQPIVSEEEWAHTKQLVDEFQASGGVGERLQKGLERRARKTENWLSEWWLKTAYLQYRQPVVIYSSPGVMLPKQDFVDLQGQLRFAAKLIEGVLDFKVMIDNETLPVEYLGGKPLCMNQYYQILSSCRVPGPKQDTVSNFSKTKKPPTHITVVHNYQFFELDVYHSDGTPLTADQIFVQLEKIWNSSLQTNKEPVGILTSNHRNSWAKAYNTLIKDKVNRDSVRSIQKSIFTVCLDATMPRVSEDVYRSHVAGQMLHGGGSRLNSGNRWFDKTLQFIVAEDGSCGLVYEHAAAEGPPIVTLLDYVIEYTKKPELVRSPMVPLPMPKKLRFNITPEIKSDIEKAKQNLSIMIQDLDITVMVFHHFGKDFPKSEKLSPDAFIQMALQLAYYRIYGQACATYESASLRMFHLGRTDTIRSASMDSLTFVKAMDDSSVTEHQKVELLRKAVQAHRGYTDRAIRGEAFDRHLLGLKLQAIEDLVSTPDIFMDTSYAIAMHFHLSTSQVPAKTDCVMFFGPVVPDGYGVCYNPMEAHINFSLSAYNSCAETNAARLAHYLEKALLDMRALLQSHPRAKLISEEDLSLISG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-naphthalen-2-yl-6-(phenylmethyl)thieno[2,3-c]pyridin-6-ium
formula_weight	352.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

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

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	585

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6. Citations (1)

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length_a	57.868 Å
length_b	84.911 Å
length_c	137.763 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.400 Å
resolution_low	29.600 Å
r_factor	0.1462
r_work	0.1451
r_free	0.1676

fit	/app/data/saxs_computation/sc/9sck/9sck.fit
pddf	/app/data/pr_computation/sc/9sck/9sck.pr.out
profile	/app/data/saxs_computation/sc/9sck/9sck.dat