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9tm1

Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand

Method: X-RAY DIFFRACTION D_max: 81.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tm1
deposition_date	2025-12-11
title	Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand
keywords	inhibitor, bromodomain, TRANSFERASE; TRANSFERASE
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	22.66 Å
rg_electron	21.94 Å
i0	45311500.00
molecular_weight	35738.0 kDa
excluded_volume	34973 Å³
envelope_volume	58155 Å³
shell_volume	22174 Å³
envelope_diameter	83.9 Å
shell_rg	28.55 Å
envelope_rg	22.08 Å
shape_rg	21.95 Å
total_rg	22.56 Å
total_atoms	2718
n_residues	312
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	81.3 Å
rg_real	22.60 Å
rg_real_error	0.74 Å
i0_real	4.5310e+07
i0_real_error	6.1200e+05
rg_reciprocal	22.61 Å
i0_reciprocal	45310000.0000
total_estimate	0.8576
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.253
kurtosis	-0.329
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	11630000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	histone acetyltransferase
formula_weight	12622.5 kDa
ec_number	2.3.1.48
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	2962

GHKEVQLKDQILGVLDYLEKQQSAWPFLKPVSLSEAPDYYDIIKEPTDILTMRRKARHGDYKTKEDFGIELKRMFDNCRLYNAPTTIYFKYANELQTLIWPKYEAI

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Escherichia coli

Entity 2 non-polymer

description	;N-[(2S)-3-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-1-(methylamino)-1-oxidanylidene-propan-2-yl]-6-methoxy-3H-imidazo[4,5-b]pyridine-7-carboxamide ;
formula_weight	387.4 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	229

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6. Citations (1)

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length_a	58.079 Å
length_b	165.488 Å
length_c	35.974 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.800 Å
resolution_low	54.860 Å
r_factor	0.2005
r_work	0.1983
r_free	0.2458

fit	/app/data/saxs_computation/tm/9tm1/9tm1.fit
pddf	/app/data/pr_computation/tm/9tm1/9tm1.pr.out
profile	/app/data/saxs_computation/tm/9tm1/9tm1.dat

Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand

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