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9v6d

;Human Ecto-5'-nucleotidase (CD73) in complex with LB10 ;

Method: X-RAY DIFFRACTION D_max: 103.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v6d
deposition_date	2025-05-27
last_revision	2026-06-03
title	;Human Ecto-5'-nucleotidase (CD73) in complex with LB10 ;
keywords	complex, 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	34.06 Å
rg_electron	33.48 Å
i0	429972000.00
molecular_weight	111570.0 kDa
excluded_volume	107750 Å³
envelope_volume	189660 Å³
shell_volume	45985 Å³
envelope_diameter	107.9 Å
shell_rg	41.33 Å
envelope_rg	33.25 Å
shape_rg	33.45 Å
total_rg	33.94 Å
total_atoms	8441
n_residues	1044
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	103.1 Å
rg_real	33.96 Å
rg_real_error	0.69 Å
i0_real	4.3000e+08
i0_real_error	7.4340e+06
rg_reciprocal	34.02 Å
i0_reciprocal	430000000.0000
total_estimate	0.6733
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	42.6 Å
skewness	0.153
kurtosis	-0.664
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	92100000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 1.000; Smooth: 0.699

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	5'-nucleotidase
formula_weight	58913.0 kDa
ec_number	3.1.3.35,3.1.3.5,3.1.3.89,3.1.3.91,3.1.3.99
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8683

WELTILHTNDVHSRLEQTSEDSSKCVNASRCMGGVARLFTKVQQIRRAEPNVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEGLIEPLLKEAKFPILSANIKAKGPLASQISGLYLPYKVLPVGDEVVGIVGYTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMDKLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVPVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLNSSIPEDPSIKADINKWRIKLDNYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHTDEMFWNHVSMCILNGGGIRSPIDERNNGTITWENLAAVLPFGGTFDLVQLKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCRVPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYISKMKVIYPAVEGRIKFSHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1073.0 kDa
src_method	man
entity_count	1

Entity 3 branched

description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	1

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	5-[6-chloranyl-5-(2-phenylethoxy)pyridazin-3-yl]-1~{H}-pyrimidine-2,4-dione
formula_weight	344.8 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	242

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6. Citations (1)

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length_a	89.160 Å
length_b	116.300 Å
length_c	118.470 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.320 Å
resolution_low	32.670 Å
r_factor	0.1961
r_work	0.1942
r_free	0.2448

fit	/app/data/saxs_computation/v6/9v6d/9v6d.fit
pddf	/app/data/pr_computation/v6/9v6d/9v6d.pr.out
profile	/app/data/saxs_computation/v6/9v6d/9v6d.dat