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9t1v

Crystal Structure of 17 bound to the PH domain of Btk

Method: X-RAY DIFFRACTION D_max: 98.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t1v
deposition_date	2025-10-22
title	Crystal Structure of 17 bound to the PH domain of Btk
keywords	Fragment based drug discovery, PH domain, Hydrolase; HYDROLASE
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	30.65 Å
rg_electron	29.82 Å
i0	165976000.00
molecular_weight	69578.0 kDa
excluded_volume	67849 Å³
envelope_volume	122290 Å³
shell_volume	33991 Å³
envelope_diameter	100.3 Å
shell_rg	37.12 Å
envelope_rg	29.39 Å
shape_rg	29.71 Å
total_rg	30.52 Å
total_atoms	5266
n_residues	622
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	98.0 Å
rg_real	30.57 Å
rg_real_error	0.61 Å
i0_real	1.6600e+08
i0_real_error	2.4990e+06
rg_reciprocal	30.61 Å
i0_reciprocal	166000000.0000
total_estimate	0.9002
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	43.3 Å
skewness	0.194
kurtosis	-0.555
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	41080000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.922

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Tyrosine-protein kinase BTK
formula_weight	19966.9 kDa
ec_number	2.7.10.2
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	5404

AAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPSFWIDGQYLCCSQTAKNAMGCQILEN

Source

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

Entity 2 non-polymer

description	(6~{R})-6-(2-chloranyl-6-fluoranyl-phenyl)-4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid
formula_weight	294.7 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	118

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6. Citations (1)

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length_a	66.820 Å
length_b	66.281 Å
length_c	79.263 Å
angle_alpha	90.00 °
angle_beta	99.95 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.410 Å
resolution_low	55.240 Å
r_factor	0.2668
r_work	0.2634
r_free	0.3286

fit	/app/data/saxs_computation/t1/9t1v/9t1v.fit
pddf	/app/data/pr_computation/t1/9t1v/9t1v.pr.out
profile	/app/data/saxs_computation/t1/9t1v/9t1v.dat