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9r3m

Structure of liver pyruvate kinase in complex with fluorescent probe 8a

Method: X-RAY DIFFRACTION D_max: 167.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3m
deposition_date	2025-05-05
last_revision	2025-08-13
title	Structure of liver pyruvate kinase in complex with fluorescent probe 8a
keywords	Pyruvate kinase, fluorescence, allosteric site, 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	53.65 Å
rg_electron	53.34 Å
i0	4093730000.00
molecular_weight	348500.0 kDa
excluded_volume	332830 Å³
envelope_volume	624810 Å³
shell_volume	93794 Å³
envelope_diameter	165.8 Å
shell_rg	60.99 Å
envelope_rg	51.76 Å
shape_rg	53.33 Å
total_rg	53.50 Å
total_atoms	26369
n_residues	3417
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	167.2 Å
rg_real	53.53 Å
rg_real_error	0.96 Å
i0_real	4.0940e+09
i0_real_error	7.7990e+07
rg_reciprocal	53.73 Å
i0_reciprocal	4095000000.0000
total_estimate	0.8717
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.2 Å
skewness	0.104
kurtosis	-0.768
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0002
highest_alpha	171200000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.445

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Isoform L-type of Pyruvate kinase PKLR
formula_weight	48285.4 kDa
ec_number	2.7.1.40
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	28711

GSMEGPAGYLRRADVAQLTQELGTAFFQQQQLPAAMADTFLEHLCLLDIDSEPVAARSTSIIATIGPASRSVERLKEMIKAGMNIARLNFSHGSHEYHAESIANVREAVESFAGSPLSYRPVAIALDTKGPGSGPGLSEQDVRDLRFGVEHGVDIVFASFVRKASDVAAVRAALGPEGHGIKIISKIENHEGVKRFDEILEVSDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNLAGKPVVCATQMLESMITKPRPTRAETSDVANAVLDGADCIMLSGETAKGNFPVEAVKMQHAIAREAEAAVYHRQLFEELRRAAPLSRDPTEVTAIGAVEAAFKCCAAAIIVLTTTGRSAQLLSRYRPRAAVIAVTRSAQAARQVHLCRGVFPLLYREPPEAIWADDVDRRVQFGIESGKLRGFLRVGDLVIVVTGWRPGSGYTNIMRVLSIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,6-di-O-phosphono-beta-D-fructofuranose
formula_weight	340.1 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	OXALATE ION
formula_weight	88.0 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	4-[4-[(7-piperidin-1-yl-2,1,3-benzoxadiazol-4-yl)sulfonyl]piperazin-1-yl]sulfonylbenzene-1,2-diol
formula_weight	523.6 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2108

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6. Citations (1)

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length_a	208.443 Å
length_b	112.896 Å
length_c	189.009 Å
angle_alpha	90.00 °
angle_beta	91.06 °
angle_gamma	90.00 °
z_pdb	32

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.062 Å
resolution_low	188.980 Å
r_factor	0.2005
r_work	0.1987
r_free	0.2348

fit	/app/data/saxs_computation/r3/9r3m/9r3m.fit
pddf	/app/data/pr_computation/r3/9r3m/9r3m.pr.out
profile	/app/data/saxs_computation/r3/9r3m/9r3m.dat