← Back to search

9t23

Crystal Structure of 5 bound to the PH domain of Btk

Method: X-RAY DIFFRACTION D_max: 97.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9t23
deposition_date	2025-10-22
title	Crystal Structure of 5 bound to the PH domain of Btk
keywords	Fragment based drug discovery, PH domain, Hydrolase; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.00 Å
rg_electron	30.21 Å
i0	179355000.00
molecular_weight	71769.0 kDa
excluded_volume	69715 Å³
envelope_volume	127240 Å³
shell_volume	35268 Å³
envelope_diameter	99.0 Å
shell_rg	37.24 Å
envelope_rg	29.70 Å
shape_rg	30.12 Å
total_rg	30.86 Å
total_atoms	5434
n_residues	650
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

▼

3. P(r) Analysis (GNOM)

dmax	97.8 Å
rg_real	30.92 Å
rg_real_error	0.72 Å
i0_real	1.7940e+08
i0_real_error	2.6740e+06
rg_reciprocal	30.95 Å
i0_reciprocal	179400000.0000
total_estimate	0.9042
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	42.2 Å
skewness	0.186
kurtosis	-0.586
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	34400000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.920

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Tyrosine-protein kinase BTK
formula_weight	19966.9 kDa
ec_number	2.7.10.2
mutation	C145A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,C,H,K
atom_count	5650

AAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPSFWIDGQYLCCSQTAKNAMGCQILEN

Source

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

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	(6~{R})-6-[3-(trifluoromethyl)phenyl]-4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid
formula_weight	310.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	167

▶

6. Citations (1)

▶

length_a	68.889 Å
length_b	66.269 Å
length_c	79.573 Å
angle_alpha	90.00 °
angle_beta	101.88 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.845 Å
resolution_low	33.710 Å
r_factor	0.2668
r_work	0.2650
r_free	0.3191

fit	/app/data/saxs_computation/t2/9t23/9t23.fit
pddf	/app/data/pr_computation/t2/9t23/9t23.pr.out
profile	/app/data/saxs_computation/t2/9t23/9t23.dat