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9xvs

Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xvs
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	25.38 Å
rg_electron	24.73 Å
i0	98238600.00
molecular_weight	52305.0 kDa
excluded_volume	50807 Å³
envelope_volume	83255 Å³
shell_volume	28209 Å³
envelope_diameter	90.1 Å
shell_rg	31.97 Å
envelope_rg	24.98 Å
shape_rg	24.69 Å
total_rg	25.38 Å
total_atoms	4051
n_residues	479
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	85.0 Å
rg_real	25.40 Å
rg_real_error	0.70 Å
i0_real	9.8240e+07
i0_real_error	1.4360e+06
rg_reciprocal	25.39 Å
i0_reciprocal	98240000.0000
total_estimate	0.8775
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	83.7 Å
skewness	0.414
kurtosis	-0.245
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	18170000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.986

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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	4129

MAAYKLVLIRHGESAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAKKLEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	6-chloranyl-10-oxidanylidene-1,9-diazatricyclo[6.4.1.0^{4,13}]trideca-2,4(13),5,7-tetraene-2-carboxylic acid
formula_weight	264.7 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	8

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	78

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6. Citations (1)

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length_a	82.807 Å
length_b	83.844 Å
length_c	103.263 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	2.080 Å
resolution_low	43.960 Å
r_factor	0.2069
r_work	0.2052
r_free	0.2404

fit	/app/data/saxs_computation/xv/9xvs/9xvs.fit
pddf	/app/data/pr_computation/xv/9xvs/9xvs.pr.out
profile	/app/data/saxs_computation/xv/9xvs/9xvs.dat