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9r3l

Structure of liver pyruvate kinase in complex with fluorescent probe 4d

Method: X-RAY DIFFRACTION D_max: 182.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3l
deposition_date	2025-05-05
last_revision	2025-08-13
title	Structure of liver pyruvate kinase in complex with fluorescent probe 4d
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	58.36 Å
rg_electron	58.74 Å
i0	4073490000.00
molecular_weight	347360.0 kDa
excluded_volume	331800 Å³
envelope_volume	614480 Å³
shell_volume	88951 Å³
envelope_diameter	201.2 Å
shell_rg	57.75 Å
envelope_rg	57.92 Å
shape_rg	58.73 Å
total_rg	58.74 Å
total_atoms	26349
n_residues	3407
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	182.4 Å
rg_real	58.78 Å
rg_real_error	1.52 Å
i0_real	4.0730e+09
i0_real_error	8.4990e+07
rg_reciprocal	57.96 Å
i0_reciprocal	4068000000.0000
total_estimate	0.5906
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	54.0 Å
skewness	0.448
kurtosis	-0.558
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	96250000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.925; Smooth: 0.005

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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	26951

GSMEGPAGYLRRADVAQLTQELGTAFFQQQQLPAAMADTFLEHLCLLDIDSEPVAARSTSIIATIGPASRSVERLKEMIKAGMNIARLNFSHGSHEYHAESIANVREAVESFAGSPLSYRPVAIALDTKGPGSGPGLSEQDVRDLRFGVEHGVDIVFASFVRKASDVAAVRAALGPEGHGIKIISKIENHEGVKRFDEILEVSDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNLAGKPVVCATQMLESMITKPRPTRAETSDVANAVLDGADCIMLSGETAKGNFPVEAVKMQHAIAREAEAAVYHRQLFEELRRAAPLSRDPTEVTAIGAVEAAFKCCAAAIIVLTTTGRSAQLLSRYRPRAAVIAVTRSAQAARQVHLCRGVFPLLYREPPEAIWADDVDRRVQFGIESGKLRGFLRVGDLVIVVTGWRPGSGYTNIMRVLSIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	OXALATE ION
formula_weight	88.0 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	4-[4-[[7-(azetidin-1-yl)-2,1,3-benzoxadiazol-4-yl]sulfonyl]piperazin-1-yl]sulfonylbenzene-1,2-diol
formula_weight	495.5 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

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

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	582

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6. Citations (1)

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length_a	110.880 Å
length_b	111.312 Å
length_c	118.978 Å
angle_alpha	103.60 °
angle_beta	104.13 °
angle_gamma	118.12 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.158 Å
resolution_low	105.260 Å
r_factor	0.2408
r_work	0.2391
r_free	0.2730

fit	/app/data/saxs_computation/r3/9r3l/9r3l.fit
pddf	/app/data/pr_computation/r3/9r3l/9r3l.pr.out
profile	/app/data/saxs_computation/r3/9r3l/9r3l.dat