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9r3i

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

Method: X-RAY DIFFRACTION D_max: 118.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3i
deposition_date	2025-05-05
last_revision	2025-08-13
title	Structure of liver pyruvate kinase in complex with fluorescent probe 4c
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	37.47 Å
rg_electron	36.92 Å
i0	1047920000.00
molecular_weight	172390.0 kDa
excluded_volume	164400 Å³
envelope_volume	281050 Å³
shell_volume	60839 Å³
envelope_diameter	120.1 Å
shell_rg	45.01 Å
envelope_rg	36.81 Å
shape_rg	36.90 Å
total_rg	37.27 Å
total_atoms	13054
n_residues	1696
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	118.0 Å
rg_real	37.31 Å
rg_real_error	0.75 Å
i0_real	1.0480e+09
i0_real_error	1.7750e+07
rg_reciprocal	37.42 Å
i0_reciprocal	1048000000.0000
total_estimate	0.8325
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.0 Å
skewness	0.155
kurtosis	-0.639
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	205100000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13329

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	4

Entity 3 non-polymer

description	4-[4-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]piperazin-1-yl]sulfonyl-5-pyridin-3-yl-benzene-1,2-diol
formula_weight	560.6 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	239

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6. Citations (1)

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length_a	190.121 Å
length_b	113.026 Å
length_c	140.304 Å
angle_alpha	90.00 °
angle_beta	132.05 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.579 Å
resolution_low	28.320 Å
r_factor	0.2434
r_work	0.2411
r_free	0.2914

fit	/app/data/saxs_computation/r3/9r3i/9r3i.fit
pddf	/app/data/pr_computation/r3/9r3i/9r3i.pr.out
profile	/app/data/saxs_computation/r3/9r3i/9r3i.dat

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

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