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9rft

Structure of liver pyruvate kinase in complex with Liver pyruvate kinase in complex with fluorescent probe II

Method: X-RAY DIFFRACTION D_max: 171.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rft
deposition_date	2025-06-04
last_revision	2026-04-08
title	Structure of liver pyruvate kinase in complex with Liver pyruvate kinase in complex with fluorescent probe II
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	53.51 Å
rg_electron	53.18 Å
i0	4085010000.00
molecular_weight	348250.0 kDa
excluded_volume	332650 Å³
envelope_volume	623560 Å³
shell_volume	93881 Å³
envelope_diameter	165.6 Å
shell_rg	60.83 Å
envelope_rg	51.58 Å
shape_rg	53.16 Å
total_rg	53.34 Å
total_atoms	26337
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	171.1 Å
rg_real	53.38 Å
rg_real_error	1.40 Å
i0_real	4.0850e+09
i0_real_error	7.8270e+07
rg_reciprocal	53.59 Å
i0_reciprocal	4086000000.0000
total_estimate	0.8899
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.8 Å
skewness	0.102
kurtosis	-0.759
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	174400000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.749

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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	28404

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	6-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]-2-(phenylmethyl)phthalazin-1-one
formula_weight	461.5 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1833

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6. Citations (1)

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length_a	207.920 Å
length_b	112.965 Å
length_c	188.562 Å
angle_alpha	90.00 °
angle_beta	91.44 °
angle_gamma	90.00 °
z_pdb	32

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.274 Å
resolution_low	188.500 Å
r_factor	0.2120
r_work	0.2101
r_free	0.2450

fit	/app/data/saxs_computation/rf/9rft/9rft.fit
pddf	/app/data/pr_computation/rf/9rft/9rft.pr.out
profile	/app/data/saxs_computation/rf/9rft/9rft.dat