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9r0d

;Human CD73 (ecto 5'-nucleotidase) in complex with compound 7 ;

Method: X-RAY DIFFRACTION D_max: 135.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r0d
deposition_date	2025-04-24
title	;Human CD73 (ecto 5'-nucleotidase) in complex with compound 7 ;
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	37.61 Å
rg_electron	38.18 Å
i0	420342000.00
molecular_weight	110620.0 kDa
excluded_volume	106530 Å³
envelope_volume	183540 Å³
shell_volume	43449 Å³
envelope_diameter	140.4 Å
shell_rg	40.32 Å
envelope_rg	38.21 Å
shape_rg	38.23 Å
total_rg	38.19 Å
total_atoms	8344
n_residues	1053
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	135.4 Å
rg_real	38.17 Å
rg_real_error	1.82 Å
i0_real	4.2030e+08
i0_real_error	8.0140e+06
rg_reciprocal	37.82 Å
i0_reciprocal	420200000.0000
total_estimate	0.7808
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.2 Å
skewness	0.641
kurtosis	-0.228
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	72420000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.539; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.676; Smooth: 0.856

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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	8809

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	nat
entity_count	2

Entity 5 non-polymer

description	;[[(2~{R},3~{S},4~{R},5~{R})-5-[5-chloranyl-7-[[(1~{S})-1~{H}-inden-1-yl]-methyl-amino]-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid ;
formula_weight	588.8 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	372

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6. Citations (1)

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length_a	231.987 Å
length_b	94.009 Å
length_c	55.522 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	2.400 Å
resolution_low	115.990 Å
r_factor	0.2145
r_work	0.2135
r_free	0.2546

fit	/app/data/saxs_computation/r0/9r0d/9r0d.fit
pddf	/app/data/pr_computation/r0/9r0d/9r0d.pr.out
profile	/app/data/saxs_computation/r0/9r0d/9r0d.dat