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9tsm

ProteinMPNN mutated PF3D7_1475600 (PfBDP4-BRD, 77.8% sequence identity) in complex with GSK9311

Method: X-RAY DIFFRACTION D_max: 61.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tsm
deposition_date	2025-12-30
last_revision	2026-05-13
title	ProteinMPNN mutated PF3D7_1475600 (PfBDP4-BRD, 77.8% sequence identity) in complex with GSK9311
keywords	plasmodium, bromodomain, inhibitor, complex, mutation, TRANSCRIPTION; TRANSCRIPTION
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	16.37 Å
rg_electron	15.34 Å
i0	3538650.00
molecular_weight	14604.0 kDa
excluded_volume	18857 Å³
envelope_volume	21039 Å³
shell_volume	12168 Å³
envelope_diameter	60.8 Å
shell_rg	20.59 Å
envelope_rg	15.85 Å
shape_rg	15.28 Å
total_rg	16.66 Å
total_atoms	2078
n_residues	117
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	61.6 Å
rg_real	16.42 Å
rg_real_error	0.48 Å
i0_real	3.5390e+06
i0_real_error	4.4280e+04
rg_reciprocal	16.42 Å
i0_reciprocal	3539000.0000
total_estimate	0.8020
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	17.4 Å
skewness	0.476
kurtosis	0.013
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	890600.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Bromodomain protein, putative
formula_weight	14443.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2476

GPMEKEIQEKKNEVLQEFLNKLIAFDKKRIFLYPVNVQLVPDYLNVIKEPMDFTTMKQKLKKGEYKSFEEFEKDVLLIINNCYTYNDPSTIYYKFAEDIETYYKKLKPDKEKKWKAVEE

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-[1,3-dimethyl-6-[(2R)-2-methylpiperazin-1-yl]-2-oxidanylidene-benzimidazol-5-yl]-N-ethyl-2-methoxy-benzamide
formula_weight	437.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(R,R)-2,3-BUTANEDIOL
formula_weight	90.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	321

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6. Citations (1)

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length_a	37.408 Å
length_b	32.153 Å
length_c	60.426 Å
angle_alpha	90.00 °
angle_beta	101.92 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.250 Å
resolution_low	29.560 Å
r_factor	0.1100
r_work	0.1089
r_free	0.1313

fit	/app/data/saxs_computation/ts/9tsm/9tsm.fit
pddf	/app/data/pr_computation/ts/9tsm/9tsm.pr.out
profile	/app/data/saxs_computation/ts/9tsm/9tsm.dat