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9rdf

Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV

Method: X-RAY DIFFRACTION D_max: 134.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rdf
deposition_date	2025-06-02
title	Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV
keywords	Fragment based drug discovery, kinase, Hydrolase; HYDROLASE
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	41.22 Å
rg_electron	40.92 Å
i0	1543100000.00
molecular_weight	211240.0 kDa
excluded_volume	201760 Å³
envelope_volume	358480 Å³
shell_volume	70002 Å³
envelope_diameter	140.4 Å
shell_rg	48.40 Å
envelope_rg	41.14 Å
shape_rg	40.97 Å
total_rg	41.08 Å
total_atoms	15967
n_residues	2084
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	134.9 Å
rg_real	41.17 Å
rg_real_error	1.02 Å
i0_real	1.5430e+09
i0_real_error	2.8970e+07
rg_reciprocal	41.22 Å
i0_reciprocal	1543000000.0000
total_estimate	0.8913
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.7 Å
skewness	0.281
kurtosis	-0.455
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	231800000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.879

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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	58708.3 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	17309

GSMEGPAGYLRRASVAQLTQELGTAFFQQQQLPAAMADTFLEHLCLLDIDSEPVAARSTSIIATIGPASRSVERLKEMIKAGMNIARLNFSHGSHEYHAESIANVREAVESFAGSPLSYRPVAIALDTKGPEIRTGILQGGPESEVELVKGSQVLVTVDPAFRTRGNANTVWVDYPNIVRVVPVGGRIYIDDGLISLVVQKIGPEGLVTQVENGGVLGSRKGVNLPGAQVDLPGLSEQDVRDLRFGVEHGVDIVFASFVRKASDVAAVRAALGPEGHGIKIISKIENHEGVKRFDEILEVSDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNLAGKPVVCATQMLESMITKPRPTRAETSDVANAVLDGADCIMLSGETAKGNFPVEAVKMQHAIAREAEAAVYHRQLFEELRRAAPLSRDPTEVTAIGAVEAAFKCCAAAIIVLTTTGRSAQLLSRYRPRAAVIAVTRSAQAARQVHLCRGVFPLLYREPPEAIWADDVDRRVQFGIESGKLRGFLRVGDLVIVVTGWRPGSGYTNIMRVLSIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	6-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]-2-(1~{H}-pyrazol-4-ylmethyl)isoquinolin-1-one
formula_weight	450.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	OXALATE ION
formula_weight	88.0 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	1,6-di-O-phosphono-beta-D-fructofuranose
formula_weight	340.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1145

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6. Citations (1)

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length_a	200.183 Å
length_b	97.584 Å
length_c	136.398 Å
angle_alpha	90.00 °
angle_beta	118.53 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.620 Å
resolution_low	78.650 Å
r_factor	0.2380
r_work	0.2378
r_free	0.2772

fit	/app/data/saxs_computation/rd/9rdf/9rdf.fit
pddf	/app/data/pr_computation/rd/9rdf/9rdf.pr.out
profile	/app/data/saxs_computation/rd/9rdf/9rdf.dat