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9qdb

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 29d

Method: X-RAY DIFFRACTION D_max: 71.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdb
deposition_date	2025-03-06
title	The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 29d
keywords	Inhibitor, Complex, FKBP, ISOMERASE; ISOMERASE
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	21.73 Å
rg_electron	20.69 Å
i0	11871300.00
molecular_weight	27250.0 kDa
excluded_volume	34638 Å³
envelope_volume	41238 Å³
shell_volume	17217 Å³
envelope_diameter	72.0 Å
shell_rg	26.22 Å
envelope_rg	20.62 Å
shape_rg	20.70 Å
total_rg	21.46 Å
total_atoms	3833
n_residues	256
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	71.1 Å
rg_real	21.75 Å
rg_real_error	0.50 Å
i0_real	1.1870e+07
i0_real_error	1.6620e+05
rg_reciprocal	21.75 Å
i0_reciprocal	11870000.0000
total_estimate	0.8859
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.316
kurtosis	-0.544
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	2083000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Peptidyl-prolyl cis-trans isomerase FKBP5
formula_weight	14004.0 kDa
ec_number	5.2.1.8
mutation	A19T, C103A, C107I
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3907

GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	;(2~{S},9~{S},12~{R})-2-cyclohexyl-20,23-dimethoxy-12-methyl-11,14,18-trioxa-4-azatricyclo[17.2.2.0^{4,9}]tricosa-1(22),19(23),20-triene-3,10-dione ;
formula_weight	503.6 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	74

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6. Citations (1)

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length_a	48.628 Å
length_b	48.628 Å
length_c	194.979 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.050 Å
resolution_low	41.198 Å
r_factor	—
r_work	0.2151
r_free	0.2610

fit	/app/data/saxs_computation/qd/9qdb/9qdb.fit
pddf	/app/data/pr_computation/qd/9qdb/9qdb.pr.out
profile	/app/data/saxs_computation/qd/9qdb/9qdb.dat

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 29d

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction