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9r0g

;Human CD73 (ecto 5'-nucleotidase) in complex with compound 21 ;

Method: X-RAY DIFFRACTION D_max: 131.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r0g
deposition_date	2025-04-24
title	;Human CD73 (ecto 5'-nucleotidase) in complex with compound 21 ;
keywords	;5'-NUCLEOTIDASE, HYDROLASE, PHOSPHATASE, INHIBITOR ;; 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	37.38 Å
rg_electron	37.88 Å
i0	422025000.00
molecular_weight	110650.0 kDa
excluded_volume	106450 Å³
envelope_volume	185200 Å³
shell_volume	43830 Å³
envelope_diameter	139.3 Å
shell_rg	40.55 Å
envelope_rg	37.97 Å
shape_rg	37.92 Å
total_rg	37.92 Å
total_atoms	8344
n_residues	1052
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	131.9 Å
rg_real	37.90 Å
rg_real_error	1.28 Å
i0_real	4.2200e+08
i0_real_error	7.8940e+06
rg_reciprocal	37.58 Å
i0_reciprocal	421900000.0000
total_estimate	0.7861
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.4 Å
skewness	0.629
kurtosis	-0.254
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	84010000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.583; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.728; Smooth: 0.741

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	5'-nucleotidase
formula_weight	59318.5 kDa
ec_number	3.1.3.35,3.1.3.5,3.1.3.89,3.1.3.91,3.1.3.99
mutation	N53D, N333D, N403D
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8552

LASMWELTILHTNDVHSRLEQTSEDSSKCVDASRCMGGVARLFTKVQQIRRAEPNVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEGLIEPLLKEAKFPILSANIKAKGPLASQISGLYLPYKVLPVGDEVVGIVGYTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMDKLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVPVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLNSSIPEDPSIKADINKWRIKLDDYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHTDEMFWNHVSMCILNGGGIRSPIDERNDGTITWENLAAVLPFGGTFDLVQLKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCRVPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYISKMKVIYPAVEGRIKFSHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

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

Entity 5 non-polymer

description	;[(2~{R})-2-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-(cyclopentylamino)pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]-1-oxidanyl-3-(2~{H}-1,2,3,4-tetrazol-5-yl)propan-2-yl]phosphonic acid ;
formula_weight	575.9 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	199

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6. Citations (1)

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length_a	230.585 Å
length_b	94.048 Å
length_c	54.860 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.430 Å
resolution_low	115.290 Å
r_factor	0.2116
r_work	0.2106
r_free	0.2508

fit	/app/data/saxs_computation/r0/9r0g/9r0g.fit
pddf	/app/data/pr_computation/r0/9r0g/9r0g.pr.out
profile	/app/data/saxs_computation/r0/9r0g/9r0g.dat