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9rmo

Crystal Structure of 31 bound to the PH domain of Btk

Method: X-RAY DIFFRACTION D_max: 99.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rmo
deposition_date	2025-06-18
title	Crystal Structure of 31 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	31.26 Å
rg_electron	30.41 Å
i0	171047000.00
molecular_weight	70427.0 kDa
excluded_volume	68493 Å³
envelope_volume	125130 Å³
shell_volume	34121 Å³
envelope_diameter	100.0 Å
shell_rg	37.70 Å
envelope_rg	29.93 Å
shape_rg	30.29 Å
total_rg	31.11 Å
total_atoms	5314
n_residues	630
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	99.4 Å
rg_real	31.18 Å
rg_real_error	0.61 Å
i0_real	1.7100e+08
i0_real_error	2.5110e+06
rg_reciprocal	31.22 Å
i0_reciprocal	171100000.0000
total_estimate	0.8995
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.8 Å
skewness	0.170
kurtosis	-0.582
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	43600000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.921

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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	19950.9 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	5612

AAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPAFWIDGQYLCCSQTAKNAMGCQILEN

Source

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

Entity 2 non-polymer

description	(6~{S})-6-(5-bromanylthiophen-2-yl)-6,7-dihydro-1-benzofuran-3-carboxylic acid
formula_weight	325.2 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	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	292

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6. Citations (1)

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length_a	68.924 Å
length_b	66.883 Å
length_c	79.936 Å
angle_alpha	90.00 °
angle_beta	100.11 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	56.530 Å
r_factor	0.2531
r_work	0.2510
r_free	0.2933

fit	/app/data/saxs_computation/rm/9rmo/9rmo.fit
pddf	/app/data/pr_computation/rm/9rmo/9rmo.pr.out
profile	/app/data/saxs_computation/rm/9rmo/9rmo.dat