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9vg4

Structural complex of FTO bound with 8j

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	9vg4
deposition_date	2025-06-12
title	Structural complex of FTO bound with 8j
keywords	FTO, 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	24.91 Å
rg_electron	24.47 Å
i0	72366800.00
molecular_weight	44603.0 kDa
excluded_volume	43125 Å³
envelope_volume	71709 Å³
shell_volume	25072 Å³
envelope_diameter	85.4 Å
shell_rg	31.10 Å
envelope_rg	24.78 Å
shape_rg	24.39 Å
total_rg	25.14 Å
total_atoms	3355
n_residues	430
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	25.02 Å
rg_real_error	0.73 Å
i0_real	7.2370e+07
i0_real_error	1.0970e+06
rg_reciprocal	25.00 Å
i0_reciprocal	72370000.0000
total_estimate	0.7885
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.6 Å
skewness	0.453
kurtosis	-0.378
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	15900000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 0.980; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Alpha-ketoglutarate-dependent dioxygenase FTO
formula_weight	54636.6 kDa
ec_number	1.14.11.-,1.14.11.53
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3392

GSHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGQDEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	2-[[2-chloranyl-6-ethyl-4-[2-[[(E)-4-oxidanyl-4-oxidanylidene-but-2-enoyl]amino]ethylcarbamoyl]phenyl]amino]benzoic acid
formula_weight	459.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	N-OXALYLGLYCINE
formula_weight	147.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	35

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6. Citations (1)

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length_a	141.830 Å
length_b	141.830 Å
length_c	83.390 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	9

space_group	H 3
int_tables_number	146
crystal_system	—

resolution	2.300 Å
resolution_low	70.920 Å
r_factor	0.2049
r_work	0.2025
r_free	0.2518

fit	/app/data/saxs_computation/vg/9vg4/9vg4.fit
pddf	/app/data/pr_computation/vg/9vg4/9vg4.pr.out
profile	/app/data/saxs_computation/vg/9vg4/9vg4.dat