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- PDB-9hj4: Crystal structure of CD73 (ecto-5'-nucleotidase) complexed to 8-b... -

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Basic information

Entry
Database: PDB / ID: 9hj4
TitleCrystal structure of CD73 (ecto-5'-nucleotidase) complexed to 8-butylthioadenosine 5'monophosphate (compound 3 in publication) in the open enzyme state
Components5'-nucleotidase
KeywordsHYDROLASE / CD73 / 5'nucleotidase / dizinc center / nucleotide derivative / AMP derivative
Function / homology
Function and homology information


thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process / : / IMP-specific 5'-nucleotidase / : / Nicotinate metabolism / Purine catabolism / : / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / ATP metabolic process / Purinergic signaling in leishmaniasis infection / calcium ion homeostasis / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.06 Å
AuthorsStrater, N. / Moschuetz, S. / Bi, C. / Muller, C.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)335447717 Germany
CitationJournal: Acs Pharmacol Transl Sci / Year: 2025
Title: Synthesis, Characterization, Interactions, and Immunomodulatory Function of Ectonucleotidase CD39/CD73 Inhibitor 8-Butylthioadenosine 5'-Monophosphate.
Authors: Bi, C. / Mirza, S. / Baburi, H. / Schakel, L. / Winzer, R. / Moschutz, S. / Keetz, K. / Lopez, V. / Pelletier, J. / Sevigny, J. / Schulze Zur Wiesch, J. / Claff, T. / Tolosa, E. / ...Authors: Bi, C. / Mirza, S. / Baburi, H. / Schakel, L. / Winzer, R. / Moschutz, S. / Keetz, K. / Lopez, V. / Pelletier, J. / Sevigny, J. / Schulze Zur Wiesch, J. / Claff, T. / Tolosa, E. / Namasivayam, V. / Strater, N. / Muller, C.E.
History
DepositionNov 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3587
Polymers60,3631
Non-polymers9956
Water11,476637
1
A: 5'-nucleotidase
hetero molecules

A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,71614
Polymers120,7272
Non-polymers1,98912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4260 Å2
ΔGint-184 kcal/mol
Surface area39280 Å2
Unit cell
Length a, b, c (Å)67.251, 131.045, 66.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-973-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5'-nucleotidase / 5'-NT / Ecto-5'-nucleotidase


Mass: 60363.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P21589, 5'-nucleotidase

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Non-polymers , 6 types, 643 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-A1IVB / [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-butylsulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 435.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N5O7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 7 % PEG 6.000, 0.1 M MES pH 6.2, 20 % PEG 200, 10 mM ligand

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.06→38.32 Å / Num. obs: 231551 / % possible obs: 92.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.019 / Rrim(I) all: 0.063 / Net I/σ(I): 18.2
Reflection shellResolution: 1.06→1.11 Å / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 11578 / CC1/2: 0.597 / Rpim(I) all: 0.458 / Rrim(I) all: 1.229

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.06→38.32 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1479 11648 5.03 %
Rwork0.1301 --
obs0.131 231542 86.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.06→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 53 637 4735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074589
X-RAY DIFFRACTIONf_angle_d0.9976287
X-RAY DIFFRACTIONf_dihedral_angle_d12.3071753
X-RAY DIFFRACTIONf_chiral_restr0.084691
X-RAY DIFFRACTIONf_plane_restr0.008854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.070.2839590.27171052X-RAY DIFFRACTION13
1.07-1.080.3128900.26111757X-RAY DIFFRACTION21
1.08-1.090.26731710.26963119X-RAY DIFFRACTION37
1.09-1.110.24282720.25284475X-RAY DIFFRACTION54
1.11-1.120.25682180.22685137X-RAY DIFFRACTION61
1.12-1.140.22562830.19935719X-RAY DIFFRACTION68
1.14-1.150.20683450.1766517X-RAY DIFFRACTION78
1.15-1.170.18624160.15847531X-RAY DIFFRACTION90
1.17-1.190.16694350.14548117X-RAY DIFFRACTION97
1.19-1.210.1564310.1358261X-RAY DIFFRACTION98
1.21-1.230.15354630.13068192X-RAY DIFFRACTION98
1.23-1.250.14924330.12458225X-RAY DIFFRACTION98
1.25-1.280.14344480.12168223X-RAY DIFFRACTION98
1.28-1.30.14144580.11798249X-RAY DIFFRACTION98
1.3-1.330.13564410.11838229X-RAY DIFFRACTION98
1.33-1.360.13994100.11918275X-RAY DIFFRACTION98
1.36-1.40.13754660.11828270X-RAY DIFFRACTION99
1.4-1.430.12194380.11038391X-RAY DIFFRACTION99
1.43-1.480.12363740.10398428X-RAY DIFFRACTION99
1.48-1.520.12064010.10138421X-RAY DIFFRACTION99
1.52-1.580.11864740.10238367X-RAY DIFFRACTION99
1.58-1.640.12664090.10678451X-RAY DIFFRACTION99
1.64-1.720.13064450.1148434X-RAY DIFFRACTION99
1.72-1.810.13394740.11868392X-RAY DIFFRACTION99
1.81-1.920.13194440.11758468X-RAY DIFFRACTION100
1.92-2.070.12324400.12268547X-RAY DIFFRACTION100
2.07-2.280.13814780.11898514X-RAY DIFFRACTION100
2.28-2.60.14174610.12548597X-RAY DIFFRACTION100
2.6-3.280.15375000.13938607X-RAY DIFFRACTION100
3.28-38.320.17354710.14798929X-RAY DIFFRACTION99

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