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9xw4

Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor

Method: X-RAY DIFFRACTION D_max: 87.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xw4
deposition_date	2025-11-27
title	Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor
keywords	PGAM1, ISOMERASE, Inhibitor; ISOMERASE
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	25.26 Å
rg_electron	24.67 Å
i0	98733400.00
molecular_weight	52386.0 kDa
excluded_volume	50768 Å³
envelope_volume	81828 Å³
shell_volume	27888 Å³
envelope_diameter	90.0 Å
shell_rg	31.78 Å
envelope_rg	24.92 Å
shape_rg	24.63 Å
total_rg	25.31 Å
total_atoms	4024
n_residues	477
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	87.2 Å
rg_real	25.30 Å
rg_real_error	0.57 Å
i0_real	9.8730e+07
i0_real_error	1.4040e+06
rg_reciprocal	25.29 Å
i0_reciprocal	98730000.0000
total_estimate	0.8662
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.427
kurtosis	-0.227
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	17330000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phosphoglycerate mutase 1
formula_weight	29917.1 kDa
ec_number	5.4.2.11,5.4.2.4
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C
atom_count	4252

MAAYKLVLIRHGESAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAKKLEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	7-bromanyl-5-chloranyl-3-phenylazanyl-1-benzothiophene-2-carboxylic acid
formula_weight	382.7 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	228

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6. Citations (1)

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length_a	81.622 Å
length_b	86.376 Å
length_c	100.644 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.110 Å
resolution_low	43.190 Å
r_factor	0.1836
r_work	0.1822
r_free	0.2093

fit	/app/data/saxs_computation/xw/9xw4/9xw4.fit
pddf	/app/data/pr_computation/xw/9xw4/9xw4.pr.out
profile	/app/data/saxs_computation/xw/9xw4/9xw4.dat